PHYLIP
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| :Some very ''popular'' programs are: | :Some very ''popular'' programs are: | ||
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/protpars.php PROTPARS]''': estimates phylogenies from protein sequences using the parsimony method. |
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnapars.php DNAPARS]''': estimates phylogenies from DNA sequences using the parsimony method. |
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnaml.php DNAML]''': estimates phylogenies from nucleotide sequences by maximum likelihood. |
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/dnamlk.php DNAMLK]''': same as DNAML but assumes a molecular clock. |
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/proml.php PROML]''': estimates phylogenies from protein amino acid sequences by maximum likelihood. |
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/promlk.php PROMLK]''': same as PROML but assumes a molecular clock. |
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/fitch.php FITCH]''': estimates phylogenies from distance matrix data under the ''additive tree model'' according to which the distances are expected to equal the sums of branch lengths between the species. |
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/kitsch.php KITSCH]''':estimates phylogenies from distance matrix data under the ''ultrametric'' model which is the same as the additive tree model except that an evolutionary clock is assumed. |
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/drawgram.php DRAWGRAM]''': plots rooted phylogenies, cladograms, circular trees and phenograms. |
| - | :*'''[http://bioinfo.ceinge.unina.it/ | + | :*'''[http://bioinfo.ceinge.unina.it/tools/winterf/drawtree.php DRAWTREE]''': similar to DRAWGRAM but plots unrooted phylogenies. |
| :A detailed explanation of all PHYLIP programs is available [http://bioinfo.ceinge.unina.it/help/phylip/ here] | :A detailed explanation of all PHYLIP programs is available [http://bioinfo.ceinge.unina.it/help/phylip/ here] | ||
Revision as of 13:15, 20 June 2007
PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies. PHYLIP (verison 3.6) is installed and run on the cluster server and is highly connected both with the Bioinformatic service and research group activity. For example, they are used to define relationships among conserved sequences in different species in evolutionary analyses.
How to reach PHYLIP
- PHYLIP programs can be searched and launched from the Bioinfo website through the PROGsDB.
- Some of the application, such as DRAWGRAM and DRAWTREE can be directly launched by CAPRI.
- In the VLS environment, the PHYLIP package is fully available for command line use in the directory /bioprogs/phylip.
Available programs
- The programs of Phylip packages use different methods, such as parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. It is able to accept different types of input data, such as molecular sequences, gene frequencies, restriction sites or distance matrices.
- Some very popular programs are:
- PROTPARS: estimates phylogenies from protein sequences using the parsimony method.
- DNAPARS: estimates phylogenies from DNA sequences using the parsimony method.
- DNAML: estimates phylogenies from nucleotide sequences by maximum likelihood.
- DNAMLK: same as DNAML but assumes a molecular clock.
- PROML: estimates phylogenies from protein amino acid sequences by maximum likelihood.
- PROMLK: same as PROML but assumes a molecular clock.
- FITCH: estimates phylogenies from distance matrix data under the additive tree model according to which the distances are expected to equal the sums of branch lengths between the species.
- KITSCH:estimates phylogenies from distance matrix data under the ultrametric model which is the same as the additive tree model except that an evolutionary clock is assumed.
- DRAWGRAM: plots rooted phylogenies, cladograms, circular trees and phenograms.
- DRAWTREE: similar to DRAWGRAM but plots unrooted phylogenies.
- A detailed explanation of all PHYLIP programs is available here
References
- Felsenstein, J PHYLIP -- Phylogeny Inference Package (Version 3.2), Cladistics 5: 164-166, 1989.
- For more details about PHYLIP, visit the PHYLIP web site
