Formats
Multilocus data is a list of sequence alignments, which is contained in DATA block of a nexus file. Commands use multilocus data are listed:
- MCMC_SEQ: Co-estimation of reticulate phylogenies (ILS & hybridization) and gene trees from multiple independent loci.
Here is an example:
Code Block | ||
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#NEXUS Begin data; Dimensions ntax=5 nchar=80; Format datatype=dna symbols="ACTG" missing=? gap=-; Matrix [YAL053W, 25, ...] Scer TCTTTATTGACGTGTATGGACAATT Spar TCTTTGTTAACGTGCATGGACAATT Smik TCCTTGCTAACATGCATGGACAATT Skud TCTTTGCTAACGTGCATGGATAATT Sbay TCTTTACTAACGTGCATGGATAACT [YAR007C, 30] Scer ATGAGCAGTGTTCAACTTTCGAGGGGCGAT Spar ATGAGCAGCGTTCAACTTTCGAAGGGCGAC Smik ATGAGCAGCGTGCAACTATCAAAGGGCGAC Skud ATGAGCAGTGTTCAACTTTCGAAGGGCGAC Sbay ATGAGCAGCGTTCAACTTTCGAAGGGCGAC [YBL015W, 25] Scer TCTAATTTGTTAAAGCAGAGAGTTA Spar TCTAATTTGTTAAAGCAGAGAGTTA Smik TCTAATTTGTTAAAACAGAGAGTTC Skud TCTAATCTGTTGAAGCAGAGAGTTA Sbay TCTAATCTGTTGAAGCAAAAAGTCA ;End; BEGIN PHYLONET; MCMC_SEQ -loci (YBL015W,YAR007C) -cl 550000 -bl 50000 -sf 5000; END; |
Mandatory info:
- number of taxon in the sequence alignments: "ntax=#numTaxon"
- the name and the length of sequences of the locus: "[#locusName, #seqLen]" or "[#locusName, #seqLen, #extraInfo]"
- the sequence alignment: "#speciesName sequence"