Major software
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Segway:
a dynamic Bayesian network for genomic segmentation and
pattern discovery
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Genomedata:
format for efficient storage of multiple tracks of numeric
data anchored to a genome
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Segtools:
exploratory analysis of genomic segmentations
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Sunflower:
an effective model for natural selection in promoters
Utilities
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Ensclip:
a tool to view web pages for Ensembl or GO accession IDs in your clipboard
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Enstag:
unique identifiers for Ensembl features
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GALAXI:
Global and Local Alignment eXcel Implementation
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Metascript:
a model of gene alignment incorporating alternative splicing
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Poly:
rapid development of embarrassingly parallelizable applications
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Renamer:
rename files according to a rule set
In addition, I have some software which is still under very active
development, but I am happy for you to use if you want to test
it. Please let me know if you are interested. Almost all of this is
written in Python unless otherwise specified.
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Autolog:
quick and easy logging setup
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Blastz:
Blastz runner and parser
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Bplite:
Use Perl's BPlite to process BLAST results into Python data structures
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Debugready:
drop running Python programs into the debugger
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Docsql:
A docstring interface to SQL databases
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Dotter:
interface for dotter images (requires PIL; includes dotter2png)
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Exonerate:
interface to exonerate
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Lagan:
interface to LAGAN
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Misc-python:
Miscellaneous tools (unsupported)
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Optbuild:
build command lines for external programs
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Path:
a packaged version of Jason Orendorff's path.py
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Plotfooter:
automatically add footers containing the last command to all graphs in R
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Pylip:
interface to PHYLIP
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Rescreen:
automatically reattach GNU Screen sessions
(works with gnome-terminal and rxvt)
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Textinput:
streamlined version of stdlib fileinput, and tab-delimited text input