Commits

Author Commit Message Labels Comments Date
Felipe Zapata
Fix arguments to the .format function in genetree.commands.sh for parallel raxml [issue #61]
Branches
issue-61
Felipe Zapata
RAxML now uses Parallel; failed runs will be skipped [issue#61]
Branches
issue-61
Felipe Zapata
Fix postassemble with new function in workflows
Branches
issue-42
Felipe Zapata
More on debugging chimera detection
Branches
issue-42
Felipe Zapata
More on debugging chimera detection
Branches
issue-42
Felipe Zapata
More on debugging chimera detection
Branches
issue-42
Felipe Zapata
More on debugging chimera detection
Branches
issue-42
Felipe Zapata
Add print statements to debug chimera detection
Branches
issue-42
Mark Howison
Fixes #58: improved multalign performance and robustness
Branches
52 branches
Mark Howison
Fixes #59: homologize appends genesets to queries
Branches
52 branches
Mark Howison
Fixes #60: bootstraps are optional in genetree
Branches
52 branches
Felipe Zapata
new step in postassemble to diagnose chimeras; still not tested [issue 42]
Branches
issue-42
Mark Howison
Fixes #56: homologize can start from existing gene sets
Branches
52 branches
Mark Howison
homologize: fixed default value for --genesets
Branches
issue-56
Mark Howison
new matrix2genes utility
Branches
issue-56
Mark Howison
multalign: fixed typo in error msg
Branches
issue-56
Mark Howison
new utility for comparing histograms across homologize runs
Branches
issue-56
Mark Howison
homologize: fixed cluster parsing and blast commands for genesets
Branches
issue-56
Mark Howison
homologize: renamed --supermatrices to --genesets
Branches
issue-56
Mark Howison
homologize: assume supermatrices are amino acid sequences
Branches
issue-56
Mark Howison
homologize: added --supermatrices option
Branches
issue-56
Mark Howison
Fixes #53: nr_annotate creates tabular blast output
Branches
54 branches
Mark Howison
Merge branch 'master' into devel
Branches
54 branches
Mark Howison
0.3.3
Mark Howison
Fixes #43: added mean bootstrap filter to genetree
Branches
54 branches
Mark Howison
agalma-test-phylogeny: last genetree stage skips filtertrees
Branches
issue-43
Mark Howison
genetree: fixed tree in report for supermatrix run
Branches
issue-43
Mark Howison
agalma-test-phylogeny: set min_support in genetree
Branches
issue-43
Mark Howison
genetree: added histogram to diagnostics for mean support
Branches
issue-43
Mark Howison
Fixes #51: removed auto-report generation in transcriptome
Branches
54 branches
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