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rachelss / SISRS

Site Identification from Short Read Sequences.
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Added flag for singleton usage #43

Closed BobLiterman closed 6 years ago

BobLiterman commented 6 years ago

Added an option (-s) for running 'loci'.

The user can now specify whether they want to use all the variable sites including singletons, or just the parsimony-informative sites.

-s 1: Data from alignment.nex, native SISRS behavior, DEFAULT -s 0: Data from alignment_pi.nex

BobLiterman commented 6 years ago

Added a new script to replace existing trim script. This script looks at all the MAFFT fa files and removes any sequences which contain only Ns or gaps. If fewer than MISSING taxa are removed, the raw alignment is stored separately, and a new alignment is written in the main folder. If more than MISSING are removed, the alignment is moved to a separate directory.