sate-dev/sate-core — Issue #9: SATe is accepting Step0 results even if it is bad
Author: smirarab
Created: 2012-02-22 23:10:06+00:00
State: open

Current SATe code seems to accept alignment/tree from step0 even if it is a bad alignment/tree.

See this log for an example:
`
SATe INFO: Reading input sequences from 'input.fasta'...
SATe INFO: Directory for temporary files created at tmp
SATe INFO: Performing initial alignment of the entire data matrix...
SATe INFO: Performing initial tree search to get starting tree...
SATe INFO: Starting SATe algorithm on initial tree...
SATe INFO: Step 0. Realigning with decomposition strategy set to longest
SATe INFO: Step 0. Alignment obtained. Tree inference beginning...
SATe INFO: realignment accepted.
SATe INFO: current score: -96055.1834, best score: -93826.1054
SATe INFO: Writing final alignment to sateout/aligned.fasta.marker001.input.aln
SATe INFO: Writing final tree to sateout/aligned.fasta.tre
SATe INFO: Writing final likelihood score to sateout/aligned.fasta.score
SATe INFO: checkpoint dump file removed: checkpoint.dump
SATe INFO: Total time spent: 7364.14707279s
SATe INFO: Note that temporary files from the run have not been deleted, they can be found in:
tmp/aligned.fasta/tempMTlYv3
`

Although the alignment/tree from the first step is very bad, it is accepted. This is not correct. If SATe cannot improve initial alignment/tree, it should just return those.