Additional file 2: of General continuous-time Markov model of sequence evolution via insertions/deletions: local alignment probability computation

A package (the version used for the analyses in this paper), which contains Perl modules that implement the key algorithms and formulas, as well as some main Perl scripts that we used for the actual data analyses. (The package is available under the GNU General Public License. The modules and scripts will run on a Mac OS X terminal, and were confirmed to run also on Red Had Enterprise Linux (6.4). And they will probably run on other UNIX platforms as well, although we have not tested whether they indeed do.) The package also contains Dawg control files necessary for creating the simulated MSA sets 1A, 1B, 2, 3P, 3M and 3F. The latest version of the package (“FA_LOLIPOG_P.verxxx”) will be available from the “LOLIPOG” (LOg-LIkelihood for the Pattern Of Gaps) project at the FTP repository of the Bioinformatics Organization [58]. (ZIP 7548 kb)