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.
| 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 -cl 550000 -bl 50000 -sf 5000;
END; |