| BioPerl |
| bioperl-live (core) | r16427 | |
| bioperl-db | r16429 | |
| biosql | r317 | |
| bioperl-run | r15747 | |
| perl | 5.8.8 | many goodies,
incl. Moose | |
| perl6 (Rakudo) | cloned master at 2009-06-23
00:44 | perl6 symlink in /usr/local/bin |
| parrot | r39729 | |
| DBs |
| MySQL | 5.0.51a | root sans passwd |
| Postgresql | 8.3.7 | d4t4h0und |
| Bioinformatics Apps |
| NCBI Blast | 2.2.17 | |
| bwa | 0.5.5 | |
| clustalw | 1.83 | |
| emboss | 5.0.0 | |
| exonerate | 1.4.0 | |
| hmmer | 2.3.2 | |
| hyphy | 1.00 | single thread build |
| maq | 0.7.1 | |
| muscle | 3.6 | |
| NeXML distro | r1201 | Bio::Phylo installed |
| phylip | 3.67 | component programs directly in path |
| phyml | 3.0 | built from src |
| primer3 | 1.1.1 | |
| samtools | 0.1.7a | libbam.so in /lib |
| t-coffee | 5.31 | |
| tigr-glimmer | 2.13-1 | |
| Misc Tools |
| apache2 | 2.2.8 | base install |
| build-essentials | | gcc 4.2.4 et al |
| emacs | 22.1.1 | Of course. |
| git-core | 1.5.4.3 | |
| graphviz | 2.16 | |
| libxml2 | 2.6.31 | base install |
| R | | |
| Subversion (svn) | 1.4.6 | |
| SWIG | 1.3.33 | |
bioperl-max AMI