PHYLIP

The component programs of phylip use several different formats, all of which are relatively simple. Programs for the analysis of DNA sequence alignments, protein sequence alignments, or discrete characters (e.g., morphological data) can accept those data in sequential or interleaved format, as shown below.

Sequential format:

5 42 
Turkey    AAGCTNGGGC ATTTCAGGGT GAGCCCGGGC AATACAGGGT AT 
Salmo schiAAGCCTTGGC AGTGCAGGGT GAGCCGTGGC CGGGCACGGT AT 
H. sapiensACCGGTTGGC CGTTCAGGGT ACAGGTTGGC CGTTCAGGGT AA 
Chimp     AAACCCTTGC CGTTACGCTT AAACCGAGGC CGGGACACTC AT 
Gorilla   AAACCCTTGC CGGTACGCTT AAACCATTGC CGGTACGCTT AA

Interleaved format:

5 42 
Turkey    AAGCTNGGGC ATTTCAGGGT 
Salmo schiAAGCCTTGGC 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

The numbers are the number of taxa (different species in the example shown above) followed by the number of characters (aligned nucleotides or amino acids in the case of molecular sequences). Restriction site data must include the number of enzymes as well.

Names are limited to 10 characters by default and must be blank-filled to be of that length and followed immediately by the character data using one-letter codes, although the 10 character limit name can be changed by a minor modification of the code (by changing nmlngth in phylip.h and recompiling). All printable ASCII/ISO characters are allowed names, except for parentheses ("(" and ")"), square brackets ("[" and "]"), colon (":"), semicolon (";") and comma (","). The spaces embedded in the alignment are ignored.

Many programs for phylogenetic analyses, including the commonly-used RAxML[4][5] and IQ-TREE[6] programs, use the phylip format or a minor modification of that format called the relaxed phylip format.

Relaxed phylip format (sequential):

5 42 
Turkey                  AAGCTNGGGCATTTCAGGGTGAGCCCGGGCAATACAGGGTAT 
Salmo_schiefermuelleri  AAGCCTTGGCAGTGCAGGGTGAGCCGTGGCCGGGCACGGTAT 
H_sapiens               ACCGGTTGGCCGTTCAGGGTACAGGTTGGCCGTTCAGGGTAA 
Chimp                   AAACCCTTGCCGTTACGCTTAAACCGAGGCCGGGACACTCAT 
Gorilla                 AAACCCTTGCCGGTACGCTTAAACCATTGCCGGTACGCTTAA

The primary difference in relaxed phylip format is the absence of the 10 character limit and the removal of the need to blank fill names to reach that length (although filling names to start the character matrix at the same position can improve readability for user). This example of relaxed uses underscores rather than spaces in the names and uses spaces between the names and the aligned character data; it is often good practice to avoid white space within taxon names and to separate the character data from the name when generating files. Like strict phylip format files, relaxed phylip format files can be in interleaved format and include spaces and endlines within the sequence data.

The programs that use distance data, like the neighbor program that implements the neighbor-joining method, also use a simple distance matrix format the includes only the number of taxa, their names, and numerical values for the distances:

Phylip distance matrix:

7 
Bovine    0.0000 1.6866 1.7198 1.6606 1.5243 1.6043 1.5905 
Mouse     1.6866 0.0000 1.5232 1.4841 1.4465 1.4389 1.4629 
Gibbon    1.7198 1.5232 0.0000 0.7115 0.5958 0.6179 0.5583 
Orang     1.6606 1.4841 0.7115 0.0000 0.4631 0.5061 0.4710 
Gorilla   1.5243 1.4465 0.5958 0.4631 0.0000 0.3484 0.3083 
Chimp     1.6043 1.4389 0.6179 0.5061 0.3484 0.0000 0.2692 
Human     1.5905 1.4629 0.5583 0.4710 0.3083 0.2692 0.0000

The number indicates the number of taxa and same limitations for taxon names exist. Note that this matrix is symmetric and the diagonal has values of 0 (since the distance between a taxon and itself is zero by definition).

Programs that use trees as input accept the trees in Newick format, an informal standard agreed to in 1986 by authors of seven major phylogeny packages. Output is written onto files with names like outfile and outtree. Trees written onto outtree are in the Newick format.

Many programs that convert among alignment formats will output data in phylip or relaxed phylip format. For example, conversion between the PHYLIP multiple sequence alignment format and Multi-FASTA format can done with Genozip[8] using genocat --fasta or genocat --phylip. The PAUP* software package is especially useful for converting between the Nexus format and phylip format.

• Official website
• Phylogeny Programs List: A large list of phylogeny packages with details on each one. Current count at 366.