sate-dev/sate-core — Issue #3: Multiple threads and initial alignment
Author: smirarab
Created: 2011-10-20 20:07:58+00:00
State: open

It seems that in creating the initial alignments, we don't use multiple threads, even if available. Look at this code in the mainsate:

```
for unaligned_seqs in multilocus_dataset:
job = sate_team.aligner.create_job(unaligned_seqs,
tmp_dir_par=init_aln_dir,
context_str="initalign",
delete_temps=delete_aln_temps)
_RunningJobs = job
jobq.put(job)
new_alignment = job.get_results()
_RunningJobs = None
new_alignment_list.append(new_alignment)
```
Shouldn't we break up this for loop to two loops (one for queuing, one for reading results) so that different markers could be aligned in parallel?