IPD-MHC Database

Phylogeny

The IPD-MHC Database does not provide any tools for phylogenetics analysis at this time. However, we do provide FASTA and PIR files which are suitable for use in many programs used to study phylogenetic relationships.

Clustalw

The EBI provides Clustal W which is a general purpose multiple sequence alignment program for DNA or protein sequences. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen. Evolutionary relationships can be seen by viewing Cladograms or Phylograms. Phylograms are branching diagrams (trees) assumed to be an estimate of a phylogeny, branch lengths are proportional to the amount of inferred evolutionary change. A Cladogram is a branching diagram (tree) assumed to be an estimate of a phylogeny where the branches are of equal length, thus cladograms show common ancestry, but do not indicate the amount of evolutionary "time" separating taxa.

• ClustalW
• ClustalW Help

PAUP

PAUP: Phylogenetic Analysis Using Parsimony is a program for phylogenetic analysis using parsimony, maximum likelihood, and distance methods. The program features an extensive selection of analysis options and model choices, and accommodates DNA, RNA, protein and general data types. Among the many strengths of the program are the rich array of options for dealing with phylogenetic trees including importing, combining, comparing, constraining, rooting and testing hypotheses.

• PAUP Homepage

PHYliP

PHYliP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites, distance matrices, and 0/1 discrete characters. PHYliP is the most widely-distributed phylogeny package, and competes with PAUP to be the one responsible for the largest number of published trees. PHYliP has been in distribution since 1980, and has over 6,000 registered users.

• Phylip Homepage

Download Files For Analysis

The FASTA and PIR files can be downloaded from the FTP directory which is available from the following addresses.

The files follow the following naming conventions:

• species.locus.type.format

For example for a file containing FASTA formatted Gorilla, A nucleotide sequences you would select gogo.a.nuc.fasta from the nhp directory.

Further Information

For information regarding IPD please contact IPD Support