BIRCH/BIRCH programs
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< BIRCH
- ACEDB
- Some linux-x86_64 systems don't have a 32-bit libncurses.so.5. This is required by xace. The quick fix for now is to include the 32-bit libncurses.so.5 in lib-linux-x86_64. The right way to fix this is to recompile xace as a 64-bit binary.
- FASTA
- FASTA search on GenPept fails to extract names and gi numbers.
- Fasta truncates sequence names if they're too long. May need to use uniqid.py to encode and decode names.
- add -N # option for fasta fasta/nucleotide. Also -Z option.
- XYLEM
- Get Features working with gbfetch; Find out difference between gbfetch vs. gbfetchwithparts
- Splitdb in biolegato can result in runaway jobs if run without data.
- getob - DBLINK line overwrites DEFINITION line in message file
- check for new Feature Keys
- splitdb can sometimes enter an infinite loop when called from feature
- NCBI
- Update Cn3D and add CDTree
- PHYLIP
- update to most recent version (this may be a good opportunity to re-implement these scripts using a new Python API, that could be utilized in all BIRCH methods.
- add 'gendist' to mbiolegato
- All programs that do resampling should be able to save the raw tree file
- GETTREES in tree2flat.py needs to be implemented more efficiently for translating very large treefiles
- output to TGIF using pstoedit command
- expanded functions
- tacg- the latest version gives compilation errors, and is no longer supported, so we need a replacement (ApeE?)
- Databases: standard distribution
- get XYLEM programs to work with remote database services
- Databases: add-ons
- specific documentation for
- local BLAST database installation
- local FASTA dababase installation
- specific documentation for