PHYLIP
From Wiki CEINGE
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.
[edit] How to reach PHYLIP
- PHYLIP programs can be searched and launched from the main website or 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.
[edit] 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 frequently used programs are:
- PROTPARS: estimates phylogenies from protein sequences using the parsimony method.
- DNAPARS: estimates phylogenies from DNA sequences using the parsimony method.
- 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
[edit] References
- Felsenstein, J PHYLIP -- Phylogeny Inference Package (Version 3.2), Cladistics 5: 164-166, 1989.
- For further details about PHYLIP, visit the PHYLIP web site
