Comments (1)
This issue is now solved. One of the issues was that the alignment needs to be trimmed (with --trim
) so it only encompasses the area on which the input HMM was trained. Another was possibly with Stockholm import. Stockholm is useful for testing the orientation because it exports posterior probabilities, which we use, but importing the alignment itself seems to have had some issues. We now use PHYLIP for the alignment itself.
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Related Issues (20)
- Remove dashes (-) FASTA files
- Make families.txt's for both COI-5P familys and matK_rbcL HOT 2
- Change alignment method HOT 3
- Use logging, not print statements
- OPTION: Integrate perl tool db into custom db HOT 1
- MACSE to HMM HOT 1
- raxml with parwise alignments HOT 2
- Handling empty FASTA files
- Spurious pandas dependency errors
- Implementation status beyond raxml HOT 1
- Skip `temporary_database.db` step
- Incompatible dependency graphs across rules HOT 1
- Data thinning
- Additional indexes needed
- RAxML placement and branch length optimization HOT 1
- Reroot unrooted raxml subtree HOT 1
- Picking exemplars HOT 2
- Submit to WorkflowHub HOT 1
- Roadmap next release
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