GenEra v1.4.1

@Eulium noticed that some of the matches against the NR have more than one NCBI taxid associated to them, leaving them out of the analysis. This new version fixed the issue of multiple taxids to include them in the gene age assignment. Thanks @Eulium !

GenEra v1.4.0

We are glad to announce that GenEra now runs really fast!
@RocesV created an additional script (FASTSTEP3R) that allows for an efficient and ultra-fast assignment of gene ages during step 3 of the pipeline. No other dependencies are required!
fast mode (-F true) will give the same result as previous versions of GenEra, with the handicap of using additional computational resources to speed up the analysis. Therefore, fast mode will be used by default for a standard GenEra run as of v.1.4.0.

GenEra v1.3.0

We added a new feature to GenEra that allows users to detect very young genes by incorporating data from different strains, varieties, or subspecies that do not have independent NCBI taxids. This is done through a phylogenetic approach using phytools and Orthofinfer as dependencies, as well as a new script in the pipeline (tree2ncbitax). This feature will prove useful to detect candidate de novo genes.

GenEra v1.2.0

Step 2 of GenEra can now be run entirely offline!
This new version of GenEra requires the file fullnamelineage.dmp contained within the latest version of the NCBI Taxonomy files. Please download this new version of the taxdump if you already installed the previous version of GenEra!

GenEra v1.1.1

• We corrected a bug in STEP 2 where GenEra would fail when giving it a raw ncbi_lineages file through a relative or absolute path when using -r.
• The pipeline also generates a unique tmp directory, even when specifying a path using -x.

GenEra v1.1.0 (release version for Genome Biology)

Several important additions were implemented for this release:

• Users can now use structural alignments with Foldseek to trace back homologs by feeding GenEra with PDB files instead of multiFASTA protein files.
• An optional step was added to reassess gene ages using JackHMMER after a first round of gene age inferences using DIAMOND (online function, significantly slows running times).
• GenEra's argument "-o" was replaced with "-u" to give additional commands to DIAMOND or Foldseek (customized search for homologs).
• GenEra's argument "-o" is now used to redirect the output files of GenEra to a user-defined directory.

GenEra v1.0.3

A couple of issues were fixed:

• Fixed an issue with STEP 2 clogging the /tmp directory with temporary files
• Fixed an issue with parameter -m, which would not filter the right percentage that was given by the user when changing the default value of 10%.

GenEra v1.0.2

Based on further benchmarking, we established "sensitive" as the default sensitivity parameter for GenEra, further increasing its speed while maintaining robust gene age inferences.

GenEra v1.0.1

New fail-safes were added to stop GenEra if it detects empty intermediate files.

GenEra v1.0.0

Initial version of genEra that was used for the preprint: https://www.biorxiv.org/content/10.1101/2022.07.07.498977v1