Recent Changes for "4. Specifying a Starting Tree" - Bodega Phylogenetics Wiki

4. Specifying a Starting Tree

2009-03-21 18:53:55

(quick edit)

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 22:	Line 22:
- We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform NPRS using the program TreeEdit.	+ We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], as well as in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform NPRS using the program TreeEdit.

4. Specifying a Starting Tree

2009-03-21 15:07:47

(quick edit)

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 50:	Line 50:
- The preceding steps provide a chronogram that can be used as a starting tree in our XML file.	+ The preceding steps provide a chronogram that can now be used as a starting tree in our XML file.

4. Specifying a Starting Tree

2009-03-21 15:07:03

(quick edit)

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 57:	Line 57:
- i. Now open the file that we generated with TreeEdit in TextWrangler. Select and copy the first tree in the NEXUS file, as depicted below.	+ i. In TextWrangler, open the file that we previously generated with TreeEdit. Select and copy the first tree in the NEXUS file, as depicted below.

4. Specifying a Starting Tree

2009-03-21 15:05:13

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 50:	Line 50:
	+ The preceding steps provide a chronogram that can be used as a starting tree in our XML file. +
Line 52:	Line 54:
- The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process. - i. Add a {{{‘newick’}}} tree element to the XML file.	+ We are now ready to specify the starting tree in the XML file with the following steps. + i. Using TextWrangler, add a {{{‘newick’}}} element to the XML file, as depicted below.
Line 55:	Line 57:
- i. Open the NPRS starting tree in a text editor, then select and copy the first tree in the NEXUS file.	+ i. Now open the file that we generated with TreeEdit in TextWrangler. Select and copy the first tree in the NEXUS file, as depicted below.
Line 57:	Line 59:
- i. Paste the NPRS chronogram into the {{{‘newick’}}} tree element.	+ i. Paste the NPRS chronogram into the {{{‘newick’}}} tree element, as depicted below.
Line 59:	Line 61:
- i. Modifying the treeModel element {{{‘ text here’}}}.	+ i. Finally, specify {{{‘newick’}}} as the starting tree in the first line of the {{{‘treeModel’}}} element, as depicted below.

4. Specifying a Starting Tree

2009-03-21 14:55:50

(quick edit)

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 22:	Line 22:
- We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program TreeEdit.	+ We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform NPRS using the program TreeEdit.

4. Specifying a Starting Tree

2009-03-21 14:51:58

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 32:	Line 32:
- i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}} button, and then click {{{‘OK’}}}. These options are depicted below.	+ i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}}. These options are depicted below.
Line 35:	Line 35:
- i. The tree has now been rendered ultrametric (i.e., such that the distance from the root to each tip is equal). Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.	+ i. After clicking on the {{{‘OK’}}} button, the tree will be rendered ultrametric (i.e., such that the distance from the root to each tip is equal). Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.

4. Specifying a Starting Tree

2009-03-21 14:50:40

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 32:	Line 32:
- i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}} button, and then click {{{‘OK’}}}. You should see that the tree becomes ultrametric (i.e., such that the distance from the root to each tip is equal), as depicted below.	+ i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}} button, and then click {{{‘OK’}}}. These options are depicted below.
Line 35:	Line 35:
- i. Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.	+ i. The tree has now been rendered ultrametric (i.e., such that the distance from the root to each tip is equal). Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.

4. Specifying a Starting Tree

2009-03-21 14:47:59

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 26:	Line 26:
- i. With the cursor tool, select the branch subtending {{{‘Platanus_kerrii’}}}, which is sister to the remaining four species. You should see that the selected branch is now highlighted, as depicted below.	+ i. With the 'cursor' tool, select the branch subtending {{{‘Platanus_kerrii’}}}, which is sister to the remaining four species. You should see that the selected branch is now highlighted, as depicted below.
Line 29:	Line 29:
- i. Select the rooting tool by clicking on the icon that is sixth from the left at the top of the TreeEdit window, and click on the branch subtending {{{‘Platanus_kerrii’}}}.	+ i. Select the 'rooting' tool by clicking on the icon that is sixth from the left at the top of the TreeEdit window, and click on the branch subtending {{{‘Platanus_kerrii’}}}. You should see that the tree becomes rooted along the selected branch, as depicted below.
Line 32:	Line 32:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. Select the 'cursor' tool clicking on the icon that is first from the left at the top of the TreeEdit window. From the '''Trees''' menu, select the {{{‘Transform branch lengths...’}}} option. A window will appear listing several options: click the {{{‘Ultrametric:’}}} button, then select the {{{‘Non-parametric rate smoothing’}}} button, and then click {{{‘OK’}}}. You should see that the tree becomes ultrametric (i.e., such that the distance from the root to each tip is equal), as depicted below.
Line 35:	Line 35:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. Select the 'node information' tool clicking on the icon that is seventh from the left at the top of the TreeEdit window. You should see that the internal nodes of the tree are now numbered, as depicted below.
Line 38:	Line 38:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. Press and hold down on the 'node information' tool to display the list of options, and then scroll down to select the {{{‘Node heights’}}} option, which will display the height of the internal nodes in expected number of substitutions, as depicted below.
Line 41:	Line 41:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. With the cursor tool, select the branch that is sister to {{{‘Platanus_kerrii’}}}, (i.e., the branch subtending the clade that includes {{{‘Platanus_orientalis’}}}, {{{‘Platanus_racemosa’}}}, {{{‘Platanus_maxicana’}}}, and {{{‘Platanus_occidentalis’}}}). You should see that the selected clade is now highlighted, as depicted below.
Line 44:	Line 44:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. From the '''Trees''' menu, select the {{{‘Scale tree...’}}} option. A window will appear listing several options: click the {{{‘Scale To:’}}} button, then select the {{{‘Scale selected height to:’}}} button, and type the value {{{‘50.0’}}} in the adjacent window (this value falls within the range that we previously specified for the age of this clade in our XML file). Next, click {{{‘OK’}}}. You should see that ages of all the remaining nodes in the tree are scaled accordingly, as depicted below.
Line 47:	Line 47:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. From the '''File''' menu, select the {{{‘Export...’}}} option. An {{{‘Export Tree(s)’}}} window will appear listing several options: click to de-select the {{{‘Use Translation List for Taxon Names’}}} button, and then click {{{‘OK’}}}. An {{{‘Export Data File’}}} window will appear: specify the name and location of the tree file, and then click {{{‘OK’}}}, as depicted below.

4. Specifying a Starting Tree

2009-03-21 14:21:18

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 20:	Line 20:
- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files available ["Divergence Time Estimation (Moore)" here].	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the example data files available ["Divergence Time Estimation (Moore)" here].
Line 22:	Line 22:
- We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program TreeEdit.	+ We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm has been implemented in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program TreeEdit.
Line 24:	Line 24:
- i. Comment out the {{{‘constantSize’}}} element as depicted below.	+ i. Double click on the TreeEdit icon to launch the application. From the '''File''' menu, select the {{{‘Open...’}}} option, and navigate to the directory that contains the file {{{‘Platanus_con_tree.tre’}}}. + + i. With the cursor tool, select the branch subtending {{{‘Platanus_kerrii’}}}, which is sister to the remaining four species. You should see that the selected branch is now highlighted, as depicted below.
Line 27:	Line 29:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ i. Select the rooting tool by clicking on the icon that is sixth from the left at the top of the TreeEdit window, and click on the branch subtending {{{‘Platanus_kerrii’}}}.

4. Specifying a Starting Tree

2009-03-21 14:11:01

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 22:	Line 22:
- We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program [[File(TreeEdit.zip)]].	+ We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and in the APE package that is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program TreeEdit. +

4. Specifying a Starting Tree

2009-03-21 14:09:10

Differences for 4. Specifying a Starting Tree

No differences found!

4. Specifying a Starting Tree

2009-03-21 14:09:04

Upload of file TreeEdit.zip.

4. Specifying a Starting Tree

2009-03-21 14:08:11

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 20:	Line 20:
- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. TreeEdit	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files available ["Divergence Time Estimation (Moore)" here]. + + We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. Here we demonstrate how to perform the NPRS using the program [[File(TreeEdit.zip)]].

4. Specifying a Starting Tree

2009-03-21 14:04:06

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 20:	Line 20:
- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["#nprs" elsewhere] in this wiki. TreeEdit	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. TreeEdit

4. Specifying a Starting Tree

2009-03-21 14:03:38

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 20:	Line 20:
- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics#nprs" elsewhere] in this wiki. TreeEdit	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["#nprs" elsewhere] in this wiki. TreeEdit

4. Specifying a Starting Tree

2009-03-21 14:02:47

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 20:	Line 20:
- We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. TreeEdit	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics#nprs" elsewhere] in this wiki. TreeEdit

4. Specifying a Starting Tree

2009-03-21 13:54:52

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 6:	Line 6:
- This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis, which is included in the in the example data files for the tutorial) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file.	+ This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file.
Line 20:	Line 20:
- The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process.	+ We need to specify a starting tree that satisfies the temporal and topological constraints associated with fossil calibration. The starting tree that we will use is based on the consensus phylogram previously estimated using MrBayes, {{{‘Platanus_con_tree.tre’}}}, which is included in the in the example data files for the tutorial. We will transform this phylogram (in which the branch lengths reflect the expected number of substitutions per site) into a chronogram (in which the branch lengths are proportional to absolute time) using nonparametric rate smoothing (NPRS). The NPRS algorithm is implemented in in several programs, including the original implementation in [http://loco.biosci.arizona.edu/r8s/ r8s], and the more recent implementation in R which is described ["II. Tree Basics" elsewhere] in this wiki. TreeEdit

4. Specifying a Starting Tree

2009-03-21 12:49:52

(quick edit)

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 58:	Line 58:
- ===== '''Ready to roll! (Finally) ''' =====	+ ===== '''Ready to roll! (At last!) ''' =====

4. Specifying a Starting Tree

2009-03-21 12:35:31

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 23:	Line 23:
- ==== - ii. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 26:	Line 26:
- ==== - iii. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 29:	Line 29:
- ==== - iv. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 32:	Line 32:
- ==== - v. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 35:	Line 35:
- ==== - vi. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 38:	Line 38:
- ==== - vii. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 41:	Line 41:
- ==== - viii. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ + i. Comment out the {{{‘coalescentTree’}}} element as depicted below.

4. Specifying a Starting Tree

2009-03-21 12:34:22

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 24:	Line 24:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ ii. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 27:	Line 27:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ iii. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 30:	Line 30:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ iv. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 33:	Line 33:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ v. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 36:	Line 36:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ vi. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 39:	Line 39:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ vii. Comment out the {{{‘coalescentTree’}}} element as depicted below.
Line 42:	Line 42:
- i. Comment out the {{{‘coalescentTree’}}} element as depicted below.	+ viii. Comment out the {{{‘coalescentTree’}}} element as depicted below.

4. Specifying a Starting Tree

2009-03-21 12:31:52

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 56:	Line 56:
	+ + ===== + ===== '''Ready to roll! (Finally) ''' ===== + We're finally ready to initiate the BEAST analysis, which we will describe in the ["5. Running a BEAST Analysis" next] part of the tutorial.

4. Specifying a Starting Tree

2009-03-21 12:28:48

Differences for 4. Specifying a Starting Tree

No differences found!

4. Specifying a Starting Tree

2009-03-21 12:28:40

Upload of image starting_tree.png.

4. Specifying a Starting Tree

2009-03-21 12:28:27

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 51:	Line 51:
- \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\|	+ \|\|<:>[[Image(starting_tree.png, thumbnail, 650, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-21 12:20:55

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 44:	Line 44:
- ==== - i. Comment out the {{{‘coalescentTree’}}} element as depicted below. - \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\|
Line 53:	Line 50:
- i. Copy the NPRS chronogram into the {{{‘newick’}}} tree element.	+ i. Open the NPRS starting tree in a text editor, then select and copy the first tree in the NEXUS file. + \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\| + i. Paste the NPRS chronogram into the {{{‘newick’}}} tree element.

4. Specifying a Starting Tree

2009-03-21 12:17:40

Upload of image newick_1.png.

4. Specifying a Starting Tree

2009-03-21 12:17:40

Image newick_1.png deleted.

4. Specifying a Starting Tree

2009-03-21 12:16:22

Differences for 4. Specifying a Starting Tree

No differences found!

4. Specifying a Starting Tree

2009-03-21 12:16:15

Upload of image newick_1.png.

4. Specifying a Starting Tree

2009-03-21 12:15:44

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 19:	Line 19:
- ===== '''Step 2: Title for step 2''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_2.png, thumbnail, 500, noborder)]]\|\|	+ ===== '''Step 2: Preparing a user-specified starting tree''' ===== + The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process. + i. Comment out the {{{‘constantSize’}}} element as depicted below. + \|\|<:>[[Image(tree_1.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_2.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_3.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_5.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_6.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_7.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_8.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_9.png, thumbnail, 500, noborder)]]\|\| + ==== + i. Comment out the {{{‘coalescentTree’}}} element as depicted below. + \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\|
Line 24:	Line 49:
- ===== '''Step 3: Title for step 3''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_3.png, thumbnail, 555, noborder)]]\|\| - - ==== - ===== '''Step 4: Title for step 4''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_5.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== Step 5: Title for step 5 ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_6.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== '''Step 6: Title for step 6''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_7.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== '''Step 7: Title for step 7''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_8.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== '''Step 8: Title for step 8''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_9.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== '''Step 9: Title for step 9''' ===== - The next step {{{‘text here’}}}. - \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\| - - ==== - ===== Specifying a starting tree ===== - How to enforce the monophyly of a specified clade {{{‘text here’}}}. - i. Commenting out the coalescent starting tree part 1: the constantSize element {{{‘ text here’}}}. - \|\|<:>[[Image(tree_block1.png, noborder)]]\|\| - i. Commenting out the coalescent starting tree part 2: the coalescentTree element {{{‘ text here’}}}. - \|\|<:>[[Image(tree_block2.png, noborder)]]\|\| - i. Specifying a newick tree element {{{‘ text here’}}}.	+ ===== '''Step 3: Adding the user-specified starting tree to the XML file''' ===== + The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process. + i. Add a {{{‘newick’}}} tree element to the XML file. + \|\|<:>[[Image(newick_1.png, noborder)]]\|\| + i. Copy the NPRS chronogram into the {{{‘newick’}}} tree element.

4. Specifying a Starting Tree

2009-03-21 12:08:17

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 6:	Line 6:
- This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file.	+ This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis, which is included in the in the example data files for the tutorial) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file.

4. Specifying a Starting Tree

2009-03-21 12:07:03

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 12:	Line 12:
- The XML file generated by BEAUti will include commands to generate a random starting tree using a coalescent process. The phylogeny generated under the coalescent process is likely to violate the temporal and/or topological constraints used for calibration, which will cause an error when we initiate the MCMC. Accordingly, we will ensure that the commands for generating a coalescent tree are ignored by BEAST, which could be achieved by simply removing these commands, or by commenting them from the file. In XML, a comment is initiated with {{{<!--}}} and terminated with {{{-->}}}, and can contain any characters except {{{--}}}. - i. Commenting out the coalescent starting tree part 1: the constantSize element {{{‘ text here’}}}.	+ The XML file generated by BEAUti includes commands to generate a starting tree under a stochastic coalescent process. These random starting trees are very likely to violate the temporal and/or topological constraints that we specified to calibrate divergence times, and will therefore cause an error when we attempt initiate the MCMC. Accordingly, we will ensure that BEAST will ignore the commands for generating a random coalescent tree, which could be achieved either by deleting these commands, or by commenting them from the file. In XML, a comment is initiated with {{{<!--}}} and terminated with {{{-->}}}, such that everything between these two tokens is ignored when the program is executed. There are two elements in the XML file that need to be commented out; the {{{‘constantSize’}}} and {{{‘coalescentTree’}}} elements. + i. Comment out the {{{‘constantSize’}}} element as depicted below.
Line 15:	Line 15:
- i. Commenting out the coalescent starting tree part 2: the coalescentTree element {{{‘ text here’}}}.	+ i. Comment out the {{{‘coalescentTree’}}} element as depicted below.

4. Specifying a Starting Tree

2009-03-21 11:47:00

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 11:	Line 11:
- ===== '''Step 1: Title for step 1''' ===== - The first step {{{‘text here’}}}. - \|\|<:>[[Image(tree_1.png, thumbnail, 500, noborder)]]\|\|	+ ===== '''Step 1: Commenting out the default starting tree''' ===== + The XML file generated by BEAUti will include commands to generate a random starting tree using a coalescent process. The phylogeny generated under the coalescent process is likely to violate the temporal and/or topological constraints used for calibration, which will cause an error when we initiate the MCMC. Accordingly, we will ensure that the commands for generating a coalescent tree are ignored by BEAST, which could be achieved by simply removing these commands, or by commenting them from the file. In XML, a comment is initiated with {{{<!--}}} and terminated with {{{-->}}}, and can contain any characters except {{{--}}}. + i. Commenting out the coalescent starting tree part 1: the constantSize element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block1.png, noborder)]]\|\| + i. Commenting out the coalescent starting tree part 2: the coalescentTree element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block2.png, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-21 11:29:40

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 4:	Line 4:
- This tutorial describes how to specify a starting tree for the MCMC that satisfies the temporal and topological constraints that we specified in Step 3 of the tutorial.	+ In the previous tutorial we described how to impose constraints within the XML file that collectively provide a means of calibrating divergence times. Here, we describe how to specify a starting tree for the MCMC that satisfies those temporal and topological constraints. + + This entails 3 main steps: (1) commenting out existing commands in the XML file that generate a default starting tree, (2) transforming the consensus phylogram (estimated from a previous ["MrBayes Tutorial" MrBayes] analysis) into a chronogram (which we will demonstrate using nonparametric rate smoothing algorithm implemented in TreeEdit), and (3) specifying the resulting chronogram as the starting tree in the XML file. + + Open the edited XML file in a text editor; in the following tutorial we used [http://www.barebones.com/products/TextWrangler/download.html/ TextWrangler]. Note that the screen captures below include the line numbers in the edited xml file to help you identify the location of the corresponding edits to the XML file.

4. Specifying a Starting Tree

2009-03-21 11:02:40

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 6:	Line 6:
- ===== Step 1: Title for step 1 =====	+ ==== + ===== '''Step 1: Title for step 1''' =====
Line 10:	Line 11:
- ===== Step 2: Title for step 2 =====	+ ==== + ===== '''Step 2: Title for step 2''' =====
Line 14:	Line 16:
- ===== Step 3: Title for step 3 =====	+ ==== + ===== '''Step 3: Title for step 3''' =====
Line 18:	Line 21:
- ===== Step 4: Title for step 4 =====	+ ==== + ===== '''Step 4: Title for step 4''' =====
Line 22:	Line 26:
	+ ====
Line 26:	Line 31:
- ===== Step 6: Title for step 6 =====	+ ==== + ===== '''Step 6: Title for step 6''' =====
Line 30:	Line 36:
- ===== Step 7: Title for step 7 =====	+ ==== + ===== '''Step 7: Title for step 7''' =====
Line 34:	Line 41:
- ===== Step 8: Title for step 8 =====	+ ==== + ===== '''Step 8: Title for step 8''' =====
Line 38:	Line 46:
- ===== Step 9: Title for step 9 =====	+ ==== + ===== '''Step 9: Title for step 9''' =====
Line 42:	Line 51:
	+ ====

4. Specifying a Starting Tree

2009-03-20 03:16:02

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 1:	Line 1:
- -->[http://bodegaphylo.wikispot.org/3._Editing_XML_Input_File Back: Tutorial Part 3] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/5._Running_a_BEAST_Analysis Next: Tutorial Part 5]<-- -->Created by [http://www.phylodiversity.net/bmoore/ Brian Moore]<--	+ -->["3. Editing XML Input File" Back: Part 3] ["Divergence Time Estimation (Moore)" Tutorial Home] ["5. Running a BEAST Analysis" Next: Part 5]<-- -->Created by [http://www.phylodiversity.net/bmoore/ Brian Moore]<--

4. Specifying a Starting Tree

2009-03-17 16:58:45

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 16:	Line 16:
- \|\|<:>[[Image(tree_3.png, thumbnail, 560, noborder)]]\|\|	+ \|\|<:>[[Image(tree_3.png, thumbnail, 555, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-17 16:58:17

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 16:	Line 16:
- \|\|<:>[[Image(tree_3.png, thumbnail, 550, noborder)]]\|\|	+ \|\|<:>[[Image(tree_3.png, thumbnail, 560, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-17 16:57:02

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 16:	Line 16:
- \|\|<:>[[Image(tree_3.png, thumbnail, 500, noborder)]]\|\|	+ \|\|<:>[[Image(tree_3.png, thumbnail, 550, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-17 16:54:40

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 49:	Line 49:
- \|\|<:>[[Image(newick_block.png, 200, noborder)]]\|\|	+ \|\|<:>[[Image(newick_block.png, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-17 16:54:21

Differences for 4. Specifying a Starting Tree

No differences found!

4. Specifying a Starting Tree

2009-03-17 16:54:13

Upload of image newick_block.png.

4. Specifying a Starting Tree

2009-03-17 16:54:13

Image newick_block.png deleted.

4. Specifying a Starting Tree

2009-03-17 16:52:58

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 49:	Line 49:
- \|\|<:>[[Image(newick_block.png, 500, noborder)]]\|\|	+ \|\|<:>[[Image(newick_block.png, 200, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-17 16:52:32

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 49:	Line 49:
- \|\|<:>[[Image(newick_block.png, noborder)]]\|\|	+ \|\|<:>[[Image(newick_block.png, 500, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-17 16:51:17

Upload of image newick_block.png.

4. Specifying a Starting Tree

2009-03-17 16:47:31

Differences for 4. Specifying a Starting Tree

No differences found!

4. Specifying a Starting Tree

2009-03-17 16:47:23

Upload of image tree_block3.png.

4. Specifying a Starting Tree

2009-03-17 16:46:57

Upload of image tree_block2.png.

4. Specifying a Starting Tree

2009-03-17 16:46:43

Upload of image tree_block1.png.

4. Specifying a Starting Tree

2009-03-17 16:46:31

Upload of image tree_10.png.

4. Specifying a Starting Tree

2009-03-17 16:46:17

Upload of image tree_9.png.

4. Specifying a Starting Tree

2009-03-17 16:46:00

Upload of image tree_8.png.

4. Specifying a Starting Tree

2009-03-17 16:45:46

Upload of image tree_7.png.

4. Specifying a Starting Tree

2009-03-17 16:45:46

Image tree_7.png deleted.

4. Specifying a Starting Tree

2009-03-17 16:45:45

Upload of image tree_7.png.

4. Specifying a Starting Tree

2009-03-17 16:45:19

Upload of image tree_6.png.

4. Specifying a Starting Tree

2009-03-17 16:45:08

Upload of image tree_5.png.

4. Specifying a Starting Tree

2009-03-17 16:44:55

Upload of image tree_3.png.

4. Specifying a Starting Tree

2009-03-17 16:44:43

Upload of image tree_2.png.

4. Specifying a Starting Tree

2009-03-17 16:44:29

Upload of image tree_1.png.

4. Specifying a Starting Tree

2009-03-17 16:44:29

Image tree_1.png deleted.

4. Specifying a Starting Tree

2009-03-17 16:44:28

Upload of image tree_1.png.

4. Specifying a Starting Tree

2009-03-17 16:44:09

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 4:	Line 4:
- Intro text goes here.	+ This tutorial describes how to specify a starting tree for the MCMC that satisfies the temporal and topological constraints that we specified in Step 3 of the tutorial.
Line 8:	Line 8:
- \|\|<:>[[Image(step1.png, thumbnail, 500, noborder)]]\|\| -	+ \|\|<:>[[Image(tree_1.png, thumbnail, 500, noborder)]]\|\|
Line 13:	Line 12:
- \|\|<:>[[Image(step2.png, thumbnail, 500, noborder)]]\|\|	+ \|\|<:>[[Image(tree_2.png, thumbnail, 500, noborder)]]\|\| + + ===== Step 3: Title for step 3 ===== + The next step {{{‘text here’}}}. + \|\|<:>[[Image(tree_3.png, thumbnail, 500, noborder)]]\|\| + + ===== Step 4: Title for step 4 ===== + The next step {{{‘text here’}}}. + \|\|<:>[[Image(tree_5.png, thumbnail, 500, noborder)]]\|\| + + ===== Step 5: Title for step 5 ===== + The next step {{{‘text here’}}}. + \|\|<:>[[Image(tree_6.png, thumbnail, 500, noborder)]]\|\| + + ===== Step 6: Title for step 6 ===== + The next step {{{‘text here’}}}. + \|\|<:>[[Image(tree_7.png, thumbnail, 500, noborder)]]\|\| + + ===== Step 7: Title for step 7 ===== + The next step {{{‘text here’}}}. + \|\|<:>[[Image(tree_8.png, thumbnail, 500, noborder)]]\|\| + + ===== Step 8: Title for step 8 ===== + The next step {{{‘text here’}}}. + \|\|<:>[[Image(tree_9.png, thumbnail, 500, noborder)]]\|\| + + ===== Step 9: Title for step 9 ===== + The next step {{{‘text here’}}}. + \|\|<:>[[Image(tree_10.png, thumbnail, 500, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-17 16:38:09

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 2:	Line 2:
	+

4. Specifying a Starting Tree

2009-03-17 16:27:35

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 1:	Line 1:
- -->[http://bodegaphylo.wikispot.org/3._Editing_XML_Input_File Back: Tutorial Part 3] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/5._Running_a_BEAST_Analysis Next: Tutorial Part 5]<--	+ -->[http://bodegaphylo.wikispot.org/3._Editing_XML_Input_File Back: Tutorial Part 3] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/5._Running_a_BEAST_Analysis Next: Tutorial Part 5]<-- -->Created by [http://www.phylodiversity.net/bmoore/ Brian Moore]<--

4. Specifying a Starting Tree

2009-03-17 15:37:49

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 13:	Line 13:
	+ + ===== Specifying a starting tree ===== + How to enforce the monophyly of a specified clade {{{‘text here’}}}. + i. Commenting out the coalescent starting tree part 1: the constantSize element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block1.png, noborder)]]\|\| + i. Commenting out the coalescent starting tree part 2: the coalescentTree element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block2.png, noborder)]]\|\| + i. Specifying a newick tree element {{{‘ text here’}}}. + \|\|<:>[[Image(newick_block.png, noborder)]]\|\| + i. Modifying the treeModel element {{{‘ text here’}}}. + \|\|<:>[[Image(tree_block3.png, noborder)]]\|\|

4. Specifying a Starting Tree

2009-03-17 15:31:28

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 1:	Line 1:
- -->[http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree Back: Tutorial Part 4] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/5._Running_a_BEAST_Analysis Next: Tutorial Part 5]<--	+ -->[http://bodegaphylo.wikispot.org/3._Editing_XML_Input_File Back: Tutorial Part 3] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/5._Running_a_BEAST_Analysis Next: Tutorial Part 5]<--

4. Specifying a Starting Tree

2009-03-17 15:30:29

Differences for 4. Specifying a Starting Tree

Deletions are marked with - .	Additions are marked with +.
Line 1:	Line 1:
	+ -->[http://bodegaphylo.wikispot.org/4._Specifying_a_Starting_Tree Back: Tutorial Part 4] [http://bodegaphylo.wikispot.org/Divergence_Time_Estimation_%28Moore%29 Tutorial Home] [http://bodegaphylo.wikispot.org/5._Running_a_BEAST_Analysis Next: Tutorial Part 5]<-- + == Introduction == + Intro text goes here. + + ===== Step 1: Title for step 1 ===== + The first step {{{‘text here’}}}. + \|\|<:>[[Image(step1.png, thumbnail, 500, noborder)]]\|\| + + + ===== Step 2: Title for step 2 ===== + The next step {{{‘text here’}}}. + \|\|<:>[[Image(step2.png, thumbnail, 500, noborder)]]\|\|