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#20 in #sites
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82 lines
count_constant_sites
Given a FASTA file with a multiple sequence alignment of nucleotides,
this tool counts the sites in the alignment that are constant. The
output is a line suitable for use in IQTREE's -fconst
, thus 4 numbers
with commas expressing the count of As, Cs, Gs and Ts.
A constant site is one where the entire column of the alignment is one nucleotide. This tool is not case sensitive. Only As, Cs, Ts and Gs are considered (i.e. gaps and ambiguous nucleotides are not considered).
TODO:
- extend to work with protein alphabets
Dependencies
~2.6–3.5MB
~63K SLoC