Botond Sipos/Ensembl Compara

Hi David, Would it be possible to include the full results of gene/species tree reconciliation in the tabular output? So for example a file containing one line per gene tree...

Hi David, I am trying to generate OrthoXML output from the example dataset included in Orthofinder 2.5.4 with the following "made up" species list file: ``` Mycoplasma_agalactiae.faa Mycoplasma agalactiae 37...

Orthogroup not split at duplication node

2

Hi David, I have run OrhoFinder `2.5.4` on the example data with the `-y` option and otherwise default parameters. The HOGs in the file `Phylogenetic_Hierarchical_Orthogroups/N0.tsv` for the orthogroup `OG0000002` look...

Aligning to distant homologues

2

What would be a recommended setting for a slower but more sensitive alignment to distant homologues?

Bumped minimum and latest Python version for mvp-rapid

1

## Description **Related JIRA tickets:** - ENSCOMPARASW-7264 ## Overview of changes #### Change 1 Bumped minimum and latest Python version for mvp-rapid. #### Change 2 Updated ensembl-py dependency. --- For...

Use tree refinement and constraint topology in species tree pipeline

1

## Description There is a need for specifying a topology constraint in the pipeline in order to allow adding new genomes to an existing topology while keeping it fixed. **Related...

Dear maintainers, I have run FastOMA on about 2200 genomes and in order to make the run smoother I have created a customised base config. The most important change is...

Report step uses very large amount of memory

1

Hello, I have run FastOMA on about 2200 genomes. The inference of HOGs finished all right (with some tweaks in the resource config), however the `fastoma_report` step failed as it...