2xread: a simple indel coding tool

Damon P. Little1

1Lewis B. and Dorothy Cullman Program for Molecular Systematics Studies, The New York Botanical Garden, Bronx, NY, USA


This script implements the simple gap (indel) coding method of Simmons and Ochoterena (2000) in a portable command line environment. Other similar tools include GapCoder (Young and Healy 2003) and SeqState (Müller 2003). The output is in the form of a xread file that is compatible with NONA, TNT, WinClada, MacClade, Mesquite, etc.

script features

The inputs for 2xread are:
(1) A DNA or RNA alignment in FASTA or dread format (output by e.g. WinClada).
(2) Optionally, a user–defined string can be used to label positions in the matrix for future reference.

script usage

2xread in_file [stem_name]

Note that “stem_name” must be interpreted as a single token by your shell. The script prints to standard out, so a redirect operator (e.g. '>') should be used to capture the output in a file.


PERL interpreter


Little, D. P. 2005. 2xread: a simple indel coding tool. Program distributed by the author.