Changes in version 1.8.6
o option to identify sequence source
Changes in version 1.8.5
o added functions for exporting plot settings
Changes in version 1.8.4
o fixed error reading taxonNamesReduced.txt that contains "#"
o added functions for import and export taxonomy DB
Changes in version 1.8.3
o fixed bug of group comparison function
Changes in version 1.8.2
o fixed loading cluster from config file
Changes in version 1.8.1
o do not show pfam links for smart domains and vice versa
Changes in version 1.7.8
o only mainInput is required in config file
Changes in version 1.7.7
o use config file for input files, refspec selection and othes
settings
Changes in version 1.6.6
o turn off auto sizing for large number of taxa or genes (>=
10.000)
Changes in version 1.6.5
o fixed filter for "species relation"
o added midpoint colors
Changes in version 1.6.2
o increase default font size for profile and domain plot
o make links to DBs: ncbi taxonomy, ncbi protein, uniprot, pfam,
smart
Changes in version 1.6.1
o modified taxonomy ranks (ropensci#875)
o improved rank indexing function (ropensci#874)
o improved x-axis label (#116)
Changes in version 1.4.12
o domain plot works with group ID containing pipe
Changes in version 1.4.11
o added check for invalid ids in newTaxa file
Changes in version 1.4.10
o fixed bug comparing unk taxon IDs with max ncbi taxID
Changes in version 1.4.9
o fixed bug comparing taxon IDs with max ncbi taxID
Changes in version 1.4.8
o fixed bug filterProfileData (some filtered data could not be
plotted)
Changes in version 1.4.5
o Add auto sizing feature
Changes in version 1.4.4
o Fixed orthoxml parsing function
Changes in version 1.4.3
o Plot background for NA orthologs
o Fixed highlight by categories
Changes in version 1.4.2
o Fixed error when parsing large amount of new taxa
o Improved the speed of parsing new taxa
o Apply filter to refspec orthologs when not working with
strain/species
Changes in version 1.4.1
o Fixed bug data lost after filtering var2
o Add filter data to detailed plot
Changes in version 1.3.11
o Add filter number of co-orthologs to parseInfoProfile()
Changes in version 1.3.10
o Calculate percentage of present taxa after filtering of var1
and var2
o Fixed filter when working with high taxonomy ranks
Changes in version 1.2.8
o Added new NCBI taxonomy ranks (e.g. biotype, isolate,
pathogroup, ...)
o Added function to reset taxonomy data
Changes in version 1.2.7
o Solved problem with new NCBI taxonomy rank "clade" by replace
them with "norank"
Changes in version 1.2.6
o Fixed bug customized profile of subset of taxa not clickable
Changes in version 1.2.4
o Fixed bug checking invalid taxon IDs
Changes in version 1.2.1
o Fixed bug in rankIndexing and processNcbiTaxonomy
o Improved check for invalid input taxon IDs
Changes in version 1.1.12
o Added pseudo IDs for Holozoa and Holomycota clades and their
non-NCBI sub-clades
Changes in version 1.1.11
o Increased the resolution of the phylostratigraphy function
Changes in version 1.1.10
o Improved the rank indexing function
Changes in version 1.1.6
o Removed grDevices, grid, stats, utils from Imports list in
DESCRIPTION
Changes in version 1.1.5
o Added progress indicators for data loading and processing steps
o Removed shinycssloaders
Changes in version 1.1.3
o Fixed bug listing taxa by selecting a supertaxon from a higher
level
o Added message for downloading preprocessed data
Changes in version 1.1.2
o Fixed bug sorting taxa when taxonomy rank is set as strain
Changes in version 1.1.1
o Commented examples of OMA parser functions
o Turned off tests for OMA parser functions
Changes in version 0.99.31
o Submitted to Bioconductor