Supplementary Material

Introduction


These pages contain the data analysed in the paper "An algorithm for progressive multiple alignment of sequences with insertions" (PNAS 102:10557--10562) and the source code for a program implementing the described method. A detailed description of the performed analyses can be found here and figures referred in the text here.


Sequence data


The two test dataset analysed are:

The results are provided as ascii (fasta format) and pdf files.



Software


The software can be found here.

Analyses


The first three of the D-loop alignments described in the paper were generated using commands:

where -d, -t, -m and -o define the names of a data file (in fasta format), a tree file (rooted, in newick format), a HMM file and an output file (in fasta format); the meaning of flags -disable and -F, as well as the modifications to use the HKY model or to align other datasets should be obvious.