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NEWS.md

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orthologr version 0.4.2

New Function

  • diamond(), set_diamond(), diamond_best() and diamond_rec() enable a massive speed-up in pairwise sequence alignment functionalities.

New Features

  • a logo is now set for orthologr.
  • DIAMOND2 is now used by default in dNdS() and divergence_stratigraphy() unless blast is specified (aligner = "blast").

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

  • the generate_ortholog_tables() and retrieve_longest_isoforms() now include the new check_annotation() function to capture corrupt GFF or GTF files and fix them

  • adding a new argument of_path to orthofinder2() to allow users to specify their own path to their locally installed orthofinder executable

  • adding new argument task to map_generator_lnc() and orthologs_lnc() to allow users to use the full blastn range provided by blast_nucleotide_to_nucleotide()

  • adding new argument path to map_generator_lnc() to allow users to specify their local installation path of BLAST

orthologr version 0.3.0

New Functions

  • new function plot_pairwise_orthologs() allows users to plot pairwise orthologs tables for multiple pairwise comparisons

  • new function retrieve_core_orthologs() allows users to retrieve a core set of orthologous gene loci from several pairwise ortholog tables

  • new functions generate_ortholog_tables() and generate_ortholog_tables_all() allow users to generate ortholog tables by gene locus and splice varaint for a set of species

  • new function retrieve_longest_isoforms_all() allows users to specify folders and retrieve the longest splice variants for all proteomes stored in a folder

  • new functions translate_cds_to_protein() and translate_cds_to_protein_all() which translate coding sequences into amino acid sequences for single or multiple files

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

  • Fixing internal path bug that caused that wrong pal2nal paths were generated when using multiple sequence aligners -> see issue #5 (Many thanks to Dr. Mario López-Pérez)

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).