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phylip [2008/05/14 13:25] – heidiphylip [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, distance matrix methods, and likelihood. It can also compute consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees, and compute distance matrices. PHYLIP, the Phylogeny Inference Package, is a package of programs for inferring phylogenies (evolutionary trees). It can infer phylogenies by parsimony, compatibility, distance matrix methods, and likelihood. It can also compute consensus trees, compute distances between trees, draw trees, resample data sets by bootstrapping or jackknifing, edit trees, and compute distance matrices.
  
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 ===== Input Files ===== ===== Input Files =====
 +
 +
  
  
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 AATCACGGCA GCCAATCAC AATCACGGCA GCCAATCAC
 </code> </code>
-  * blanks within sequences are allowed to make them easier to read+  * extension: .txt 
 +  * blanks within sequences are allowed to make them easier to read, also digits are ignored in the sequence
   * 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: <code>Archaeopt 001100    * In the **sequential format**, the character data can run on to a new line at any time. Thus it is legal to have: <code>Archaeopt 001100 
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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:  +  * the simplest version of the input data file looks something like this: <code>
-<code>+
    6   13    6   13
 Archaeopt CGATGCTTAC CGC Archaeopt CGATGCTTAC CGC
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 </code> </code>
  
 +  * example of interleaved format: <code>
 +  5    42
 +Turkey    AAGCTNGGGC ATTTCAGGGT
 +Salmo gairAAGCCTTGGC AGTGCAGGGT
 +H. SapiensACCGGTTGGC CGTTCAGGGT
 +Chimp     AAACCCTTGC CGTTACGCTT
 +Gorilla   AAACCCTTGC CGGTACGCTT
 +
 +GAGCCCGGGC AATACAGGGT AT
 +GAGCCGTGGC CGGGCACGGT AT
 +ACAGGTTGGC CGTTCAGGGT AA
 +AAACCGAGGC CGGGACACTC AT
 +AAACCATTGC CGGTACGCTT AA
 +</code>
 +
 +  * sequential format the same sequences would be: <code>
 +  5    42
 +Turkey    AAGCTNGGGC ATTTCAGGGT
 +GAGCCCGGGC AATACAGGGT AT
 +Salmo gairAAGCCTTGGC AGTGCAGGGT
 +GAGCCGTGGC CGGGCACGGT AT
 +H. SapiensACCGGTTGGC CGTTCAGGGT
 +ACAGGTTGGC CGTTCAGGGT AA
 +Chimp     AAACCCTTGC CGTTACGCTT
 +AAACCGAGGC CGGGACACTC AT
 +Gorilla   AAACCCTTGC CGGTACGCTT
 +AAACCATTGC CGGTACGCTT AA
 +</code>
  
 ==== Distance Matrix ==== ==== Distance Matrix ====
phylip.1210764334.txt.gz · Last modified: 2008/07/22 13:30 (external edit)