phylip
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phylip [2008/05/14 13:25] – heidi | phylip [2011/07/07 12:49] (current) – heidi | ||
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- | Version 3.67 (July, 2007)\\ | + | Version 3.69 (September 2009)\\ |
PHYLIP, the Phylogeny Inference Package, is a package of programs for inferring phylogenies (evolutionary trees). It can infer phylogenies by parsimony, compatibility, | PHYLIP, the Phylogeny Inference Package, is a package of programs for inferring phylogenies (evolutionary trees). It can infer phylogenies by parsimony, compatibility, | ||
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===== Input Files ===== | ===== Input Files ===== | ||
+ | |||
+ | |||
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AATCACGGCA GCCAATCAC | AATCACGGCA GCCAATCAC | ||
</ | </ | ||
- | * blanks within sequences are allowed to make them easier to read | + | |
+ | | ||
* It is important that the number of sites in each group be the same for all species | * It is important that the number of sites in each group be the same for all species | ||
* In the **sequential format**, the character data can run on to a new line at any time. Thus it is legal to have: < | * In the **sequential format**, the character data can run on to a new line at any time. Thus it is legal to have: < | ||
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=== example: === | === example: === | ||
- | For the parsimony, compatibility and maximum likelihood programs, excluding the distance matrix methods, | + | * the simplest version of the input data file looks something like this: < |
- | < | + | |
| | ||
Archaeopt CGATGCTTAC CGC | Archaeopt CGATGCTTAC CGC | ||
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</ | </ | ||
+ | * example of interleaved format: < | ||
+ | 5 42 | ||
+ | Turkey | ||
+ | Salmo gairAAGCCTTGGC AGTGCAGGGT | ||
+ | H. SapiensACCGGTTGGC CGTTCAGGGT | ||
+ | Chimp | ||
+ | Gorilla | ||
+ | |||
+ | GAGCCCGGGC AATACAGGGT AT | ||
+ | GAGCCGTGGC CGGGCACGGT AT | ||
+ | ACAGGTTGGC CGTTCAGGGT AA | ||
+ | AAACCGAGGC CGGGACACTC AT | ||
+ | AAACCATTGC CGGTACGCTT AA | ||
+ | </ | ||
+ | |||
+ | * sequential format the same sequences would be: < | ||
+ | 5 42 | ||
+ | Turkey | ||
+ | GAGCCCGGGC AATACAGGGT AT | ||
+ | Salmo gairAAGCCTTGGC AGTGCAGGGT | ||
+ | GAGCCGTGGC CGGGCACGGT AT | ||
+ | H. SapiensACCGGTTGGC CGTTCAGGGT | ||
+ | ACAGGTTGGC CGTTCAGGGT AA | ||
+ | Chimp | ||
+ | AAACCGAGGC CGGGACACTC AT | ||
+ | Gorilla | ||
+ | AAACCATTGC CGGTACGCTT AA | ||
+ | </ | ||
==== Distance Matrix ==== | ==== Distance Matrix ==== |
phylip.1210764334.txt.gz · Last modified: 2008/07/22 13:30 (external edit)