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Changelog

Source: NEWS.md

orthologr version 0.4.3

New Function

  • deepclust() enables diamond deepclust functionalities for clustering protein sequences. Multiple input .fasta files or .fasta.gz are supported.
  • deepclust_realign() enables diamond deepclust functionalities for realigning protein sequences from the output of deepclust(). Multiple input .fasta files or .fasta.gz are supported.
  • deepclust_annotate() enables diamond deepclust functionalities for annotating protein sequences from the output of deepclust() based on user provided names for each proteome file (or the name of the proteome file if not provided). deepclust_annotate() can also be used to annotate the output of deepclust_realign(). Multiple input .fasta files or .fasta.gz are supported.

Miscellaneous

orthologr version 0.4.2

New Function

New Features

orthologr version 0.4.1

New Features

  • the divergence_stratigraphy() and divergence_map() functions now include the parameter n_quantile, which enables users to choose the number of quantiles to generate for the divergence map. This could allow users to get a higher-resolution divergence map if n_quantile is greater than 10. Alternatively, this can resolve the issue of empty divergence strata when deciling the dNdS values for closely related organisms with dNdS = 0 for over 10% of the genes.

orthologr version 0.4.0

New Functions

  • new function check_annotation() helps to detect corrupt GFF or GTF annotation files and removes such outlier lines

New Features

orthologr version 0.3.0

New Functions

New Features

  • in orthologs() the default value of delete_corrupt_cds changed from delete_corrupt_cds = TRUE to delete_corrupt_cds = FALSE to be consistent with dNdS() and divergence_stratigraphy()

  • the divergence_stratigraphy() function received a new argument dnds_est.method which now allows users to select different dNdS estimation methods when running divergence_stratigraphy() (suggested by Momir Futo)

  • the divergence_stratigraphy() function now allows to change the eval argument which wasn’t passed down to the dNdS() call within the function (Many thanks to Momir Futo)

  • the function map.generator() was renamed to map_generator_dnds() to be more consistent with the notation of other functions

  • the function map.generator.lnc() was renamed to map_generator_lnc() to be more consistent with the notation of other functions

  • the function DivergenceMap() was renamed to divergence_map() to be more consistent with the notation of other functions

  • the function DivergenceMap() was renamed to divergence_map() to be more consistent with the notation of other functions

  • the function orthologs.lnc was renamed to orthologs_lnc to be more consistent with the notation of other functions

  • the function OF2CoreOrthologs() was renamed to orthofinder2_retrieve_core_orthologs()

Removed Functions

  • the function advanced_blast() is not supported anymore and thus is not available to users anymore (please consult the metablastr package in case you need this functionality)

  • the function advanced_makedb() is not supported anymore and thus is not available to users anymore (please consult the metablastr package in case you need this functionality)

  • the function blast.nr() is not supported anymore and thus is not available to users anymore (please consult the metablastr package in case you need this functionality)

  • the function delta.blast() is not supported anymore and thus is not available to users anymore (please consult the metablastr package in case you need this functionality)

  • the function ProteinOrtho() is not supported anymore and thus is not available to users anymore

orthologr version 0.2.0

New Features

  • new function retrieve_longest_isoforms() which enables retrieval of the longest isoforms from a proteome file and save results as fasta file for downstream analyses
  • new function OF2CoreOrthologs() to retrieve core orthologs across multiple species from Orthofinder2 output
  • new function extract_features(): Helper function to extract gene loci and splice variant IDs from GFF files
  • new function filter_best_hits(): Helper function to select best BLAST hit based on minimum evalue
  • new function generate_ortholog_tables(): Generate ortholog tables by gene locus and splice varaint

orthologr version 0.1.0

New Features

  • read.cds() now trimms corrupted CDS (= CDS not divisible by 3) when delete_corrupt_cds = FALSE is specified
  • the new default value of argument delete_corrupt_cds in dNdS() is now FALSE. Thus, given the new trimming feature in read.cds(), corrupted CDS equences will be trimmed before being translated.

orthologr version 0.0.5

Bug fixes

  • The default setting of the BLAST argument max_target_seqs 1 was removed from blast_best() and blast_rec() due to the misunderstood functionality of the BLAST argument (See details here and #9 ; Many thanks to @armish)

orthologr version 0.0.4

New Features

  • Users can now control via the new delete_corrupt_cds argument in dNdS() and related downstream functions whether or not corrupted input coding sequences shall be removed prior to dN/dS inference. In case corrupted CDS exist, the dNdS() function will now generate a separate fasta file which stores all corrupted CDS so that they can be investigated. See issue #8 for details.

Function updates

  • dNdS() receives new argument delete_corrupt_cds to remove corrupted input coding sequences (delete_corrupt_cds is set to TRUE as default)

  • read.cds() receives new argument delete_corrupt_cds to remove corrupted input coding sequences (delete_corrupt_cds is set to TRUE as default)

  • cds2aa() receives new argument delete_corrupt_cds to remove corrupted input coding sequences (delete_corrupt_cds is set to TRUE as default)

  • set_blast() receives new argument delete_corrupt_cds to remove corrupted input coding sequences (delete_corrupt_cds is set to TRUE as default)

  • blast() receives new argument delete_corrupt_cds to remove corrupted input coding sequences (delete_corrupt_cds is set to TRUE as default)

  • blast_best() receives new argument delete_corrupt_cds to remove corrupted input coding sequences (delete_corrupt_cds is set to TRUE as default)

  • blast_rec() receives new argument delete_corrupt_cds to remove corrupted input coding sequences (delete_corrupt_cds is set to TRUE as default)

orthologr version 0.0.3

orthologr version 0.0.2

  • Fixing a major bug that caused KaKs_Calculator to not be able to correctly parse the kaks computation output (Many thanks to Hongyi Li who spotted the bug and found a solution).