- Rename $parameters variable so it doesn't name clash
- Give more memory
- A couple more fixes

and:

- Use pytil instead of chicken_turtle_util
- Remove unnecessary @UnresolvedImport

Only use core genes with gap positions removed. Use SPR
search. Assume resulting tree is bifurcating.

Run one per species, no chunking

Run one per species, no chunking

Single-core, only generate groups

Tree generation failed (dlcpar_search uses a recursive algorithm which
exceeds max recursion depth), so we tell OrthoFinder to generate no more
than ortho groups.

Tree generation failed (dlcpar_search uses a recursive algorithm which
exceeds max recursion depth), so we tell OrthoFinder to generate no more
than ortho groups.

Segfaults on cluster, probably due to some installed packages not
working on cluster, only on midas server

- Add cedalion-orthofinder-format-input
- Remove cedalion-format-blast
- Remove cedalion-write-sequence-ids

No output emitted when not both left and right were given