Recent Changes for "starttree program" - Bodega Phylogenetics Wiki

starttree program

TracyHeath — 2012-03-13 13:53:57

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 53:	Line 53:
	+

starttree program

TracyHeath — 2012-03-13 13:53:31

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 38:	Line 38:
- {{{ File formats:	+ {{{ File formats:
Line 40:	Line 40:
- Tree file (newick format) - ----------------------------------------------- - (((T1,T2),T3),(T4,T5));	+ Tree file (newick format) + ----------------------------------------------- + (((T1,T2),T3),(T4,T5));
Line 44:	Line 44:
- -----------------------------------------------	+ -----------------------------------------------
Line 46:	Line 46:
- Node Calibration file - -U = uniform with min and max bounds - ----------------------------------------------- - 3 - -U root 25.01 30.2 - -U T1 T3 14.22 20.532 - -U T4 T5 4.773 8.3 - -----------------------------------------------}}}	+ Node Calibration file + -U = uniform with min and max bounds + ----------------------------------------------- + 3 + -U root 25.01 30.2 + -U T1 T3 14.22 20.532 + -U T4 T5 4.773 8.3 + -----------------------------------------------}}}

starttree program

TracyHeath — 2012-03-13 13:52:43

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 19:	Line 19:
	+ Execute the program and print the menu options: + + {{{> ./starttree -h}}} +
Line 30:	Line 34:
- Execute the program and print the menu options: - - {{{> ./starttree -h}}} - -
Line 39:	Line 38:
- {{{File formats:	+ {{{ File formats:
Line 41:	Line 40:
- Tree file (newick format) - ----------------------------------------------- - (((T1,T2),T3),(T4,T5));	+ Tree file (newick format) + ----------------------------------------------- + (((T1,T2),T3),(T4,T5));
Line 45:	Line 44:
- -----------------------------------------------	+ -----------------------------------------------
Line 47:	Line 46:
- Node Calibration file - -U = uniform with min and max bounds - ----------------------------------------------- - 3 - -U root 25.01 30.2 - -U T1 T3 14.22 20.532 - -U T4 T5 4.773 8.3 - -----------------------------------------------}}}	+ Node Calibration file + -U = uniform with min and max bounds + ----------------------------------------------- + 3 + -U root 25.01 30.2 + -U T1 T3 14.22 20.532 + -U T4 T5 4.773 8.3 + -----------------------------------------------}}}

starttree program

TracyHeath — 2012-03-13 13:51:45

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 17:	Line 17:
- {{{ > chmod +x starttree}}}	+ {{{> chmod +x starttree}}}
Line 32:	Line 32:
- {{{ > ./starttree -h}}}	+ {{{> ./starttree -h}}}
Line 37:	Line 37:
- {{{ > ./starttree -hf}}}	+ {{{> ./starttree -hf}}} + + {{{File formats: + + Tree file (newick format) + ----------------------------------------------- + (((T1,T2),T3),(T4,T5)); + + ----------------------------------------------- + + Node Calibration file + -U = uniform with min and max bounds + ----------------------------------------------- + 3 + -U root 25.01 30.2 + -U T1 T3 14.22 20.532 + -U T4 T5 4.773 8.3 + -----------------------------------------------}}}

starttree program

TracyHeath — 2012-03-13 13:50:42

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 19:	Line 19:
	+ {{{ example: + + $ starttree -tre tree.phy -cal calfile.txt -out output_tree.phy -n <numtaxa> + + Here are the available options that you can change (default values are in []): + -hf : display example file formats + -tre : tree file name + -n : number of tips + -cal : file name with internal node calibratons + -out : file name for output tree** }}} +

starttree program

TracyHeath — 2012-03-13 13:49:40

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 10:	Line 10:
	+ + * Your tree must be fully bifurcating and rooted + * Your calibrations must be uniform distributions + * Calibrations cannot conflict with one another (e.g. a node cannot have a calibration that is older than the calibration on nodes older than it)

starttree program

TracyHeath — 2012-03-13 13:47:07

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 5:	Line 5:
- Source code: [[File(starttree.tar.gz)]] (Requires Unix, g++, automake, autoconf)	+ Source code (Requires Unix, g++, automake, autoconf): [[File(starttree.tar.gz)]]

starttree program

TracyHeath — 2012-03-13 13:45:24

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 23:	Line 23:
	+ + '''Primary contact:''' ["Users/TracyHeath" Tracy Heath]

starttree program

TracyHeath — 2012-03-13 13:42:26

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 5:	Line 5:
- [[File(starttree.tar.gz)]] Requirements: Unix, g++, automake, autoconf	+ Source code: [[File(starttree.tar.gz)]] (Requires Unix, g++, automake, autoconf)

starttree program

TracyHeath — 2012-03-13 13:41:43

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 5:	Line 5:
- [[File(starttree.tar.gz)]] - - Requirements: Unix, g++, automake, autoconf	+ [[File(starttree.tar.gz)]] Requirements: Unix, g++, automake, autoconf

starttree program

TracyHeath — 2012-03-13 13:41:01

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 17:	Line 17:
- '''Execute the program and print the menu options'''	+ Execute the program and print the menu options:
Line 22:	Line 22:
- '''Execute the program and print information about the file formats:'''	+ Execute the program and print information about the file formats:

starttree program

TracyHeath — 2012-03-13 13:40:31

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 13:	Line 13:
- If you downloaded the binary, you will probably have to modify it so that it is executable. Do this (in terminal, in the same directory as the binary):	+ If you downloaded the binary, you will probably have to modify it so that it is executable. Do this (in terminal, in the same directory as the binary):
Line 15:	Line 15:
- {{{ > chmod +x starttree}}}	+ {{{ > chmod +x starttree}}}
Line 19:	Line 19:
- {{{ > ./starttree -h}}}	+ {{{ > ./starttree -h}}}
Line 24:	Line 24:
- {{{ > ./starttree -hf}}}	+ {{{ > ./starttree -hf}}}

starttree program

TracyHeath — 2012-03-13 13:40:08

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 11:	Line 11:
- Instructions for using this program:	+ '''Instructions for using this program:'''
Line 13:	Line 13:
- * If you downloaded the binary, you will probably have to modify it so that it is executable. Do this (in terminal, in the same directory as the binary):	+ If you downloaded the binary, you will probably have to modify it so that it is executable. Do this (in terminal, in the same directory as the binary):
Line 17:	Line 17:
	+ '''Execute the program and print the menu options'''
Line 18:	Line 19:
	+ {{{ > ./starttree -h}}} + + + '''Execute the program and print information about the file formats:''' + + {{{ > ./starttree -hf}}}

starttree program

TracyHeath — 2012-03-13 13:37:46

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 9:	Line 9:
- The tree must be in Newick format:	+ starttree binary (Mac only): [[File(starttree)]]
Line 11:	Line 11:
- (((T1,T2),T3),(T4,T5));	+ Instructions for using this program:
Line 13:	Line 13:
- starttree binary (Mac only): [[File(starttree)]]	+ * If you downloaded the binary, you will probably have to modify it so that it is executable. Do this (in terminal, in the same directory as the binary): + + {{{ > chmod +x starttree}}} + +

starttree program

TracyHeath — 2012-03-13 09:38:49

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 13:	Line 13:
- starttree binary: [[File(starttree)]]	+ starttree binary (Mac only): [[File(starttree)]]

starttree program

TracyHeath — 2012-03-12 22:55:15

Differences for starttree program

No differences found!

starttree program

TracyHeath — 2012-03-12 22:55:06

Upload of file starttree.

starttree program

TracyHeath — 2012-03-12 22:54:29

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 12:	Line 12:
	+ + starttree binary: [[File(starttree)]]

starttree program

TracyHeath — 2012-03-04 13:18:46

Upload of file starttree.tar.gz.

starttree program

TracyHeath — 2012-03-04 13:18:30

File starttree.tar.gz deleted.

starttree program

TracyHeath — 2012-03-01 16:26:11

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 12:	Line 12:
- - - Specify the node calibrations: - 3 - -U \|\| root \|\| 25.1 33.0 - -U T1 T3 14.2 20.532 - -U T4 T5 5.1 15.89

starttree program

TracyHeath — 2012-03-01 16:24:11

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 16:	Line 16:
- -U root 25.1 33.0	+ -U \|\| root \|\| 25.1 33.0

starttree program

TracyHeath — 2012-03-01 16:21:37

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 16:	Line 16:
- -U root 25.1 33.0 - -U T1 T3 14.2 20.532 - -U T4 T5 5.1 15.89	+ -U root 25.1 33.0 + -U T1 T3 14.2 20.532 + -U T4 T5 5.1 15.89

starttree program

TracyHeath — 2012-03-01 16:20:04

Upload of file starttree.tar.gz.

starttree program

TracyHeath — 2012-03-01 16:20:04

File starttree.tar.gz deleted.

starttree program

TracyHeath — 2012-03-01 16:14:04

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 1:	Line 1:
- Download this program for generating starting trees consistent with fossil calibrations for divergence time estimation methods.	+ This is a program for generating starting trees consistent with fossil calibrations for divergence time estimation methods. + + Node heights are drawn from a uniform distribution, conditional on node age constraints provided by calibrations.

starttree program

TracyHeath — 2012-03-01 16:09:37

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 3:	Line 3:
- This program requires Unix and g++	+ [[File(starttree.tar.gz)]]
Line 5:	Line 5:
- [[File(starttree.tar.gz)]]	+ Requirements: Unix, g++, automake, autoconf + + The tree must be in Newick format: + + (((T1,T2),T3),(T4,T5)); + + + Specify the node calibrations: + 3 + -U root 25.1 33.0 + -U T1 T3 14.2 20.532 + -U T4 T5 5.1 15.89

starttree program

TracyHeath — 2012-03-01 16:04:40

Differences for starttree program

No differences found!

starttree program

TracyHeath — 2012-03-01 16:04:31

Upload of file starttree.tar.gz.

starttree program

TracyHeath — 2012-03-01 16:04:05

Differences for starttree program

Deletions are marked with - .	Additions are marked with +.
Line 1:	Line 1:
	+ Download this program for generating starting trees consistent with fossil calibrations for divergence time estimation methods. + + This program requires Unix and g++ + + [[File(starttree.tar.gz)]]