Align: a Mesquite package for aligning sequence data
The Align package provides some basic tools involving alignment of sequence data. The Align package contains:
- Tools for manual alignment
- a Move Blocks tool
- a Push Sequence tool
- commands to remove gaps en masse
- Tools for automated alignment
- a Pairwise Aligner tool
- the ability to have a nucleotide matrix realigned to match an amino acid alignment
- the ability to send a block of the matrix to ClustalW or MUSCLE to align
- Various statistics about taxa based about alignments
- the alignment score of a taxon against a reference taxon
- the ratio of the alignment score of a taxon and its reverse complement against a reference taxon; this allows one to quickly detect sequences that are reverse complements of others.
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