PHYLIP, Phylogenetic Analysis Package, BLAST, DNA Sequence, Phylogenesis from Protein Sequence Inputs

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PHYLIP

This is the most widely distributed phylogenetic analysis package. It contains 30 programmes that implement different phylogenetic analysis algorithms. Each of the programmes runs separately. Most programmes look for an input file "infile" and write an output file called "outfile", rather than entering parameters (like E value, number of returns required, etc.) as with BLAST. Following are some of the PHYLIP programmes that are used frequently for analysis of protein and DNA sequences. (i) PROTPARS infers phylogenesis from protein sequence inputs; (ii) PROTDIST computes an evolutionary distance matrix from protein sequence input; (iii) DNAPARS infers phylogenesis from DNA sequence input; (iv) NEIGHBOR infers phylogenesis from distance matrix data using either pair-wise clustering or the neighbor-joining algorithms. (v) DRA WGRAM draws a rooted tree based on output from one of the phylogeny inference programme.

Phylip is a flexible package and the programmes can be used together in many ways to analyse a set of protein or DNA sequences. For instance, with PHYLIP, one can read a multiple protein sequence alignment using PROTDIST and create a distance matrix. The distance matrix can be used as an input for NEIGHBOR to generate a phylogeny based on neighbor-joining. The phylogeny is read by DRA WGRAM to produce a rooted phylogenetic tree.

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