\name{PhyloProfilenews}
\title{PhyloProfile news}
\encoding{UTF-8}

\section{Version 1.16.0}{
  \itemize{
    \item extended options in config file
    \item option to specify IP and port
    \item able to generate domain plot from main/customized profile tab
    \item highlight multiple genes/taxa; division lines for taxon group (#110)
    \item simplify gene IDs in detailed plot; show taxonomy hierarchy (#110)
    \item option to filter features in architecture plot (#110)
    \item option to show all input taxa (#110)
    \item added more info to domain plot (e-value, bit-score, pHMM)
    \item option to specify host and port for runPhyloProfile() fn
    \item fixed bug when lowest rank is subspecies
  }
}

\section{Version 1.14.5}{
  \itemize{
    \item improved highlighted duplicated ortho IDs
  }
}

\section{Version 1.14.4}{
  \itemize{
    \item fixed bug ordering genes
    \item auto identify lowest rank
  }
}

\section{Version 1.14.2}{
  \itemize{
    \item option to use user defined taxonomy DB (#124)
  }
}

\section{Version 1.14.1}{
  \itemize{
    \item option for highlight duplicated ortholog IDs
    \item option for cluster profiles based on ortholog IDs
    \item speedup by pre-calculating taxonomy tree (#123)
    \item disable rank selection after plotting
    \item turn on profile clustering by default
    \item changed "ftp://" to "https://" for taxdmp.zip
    \item fixed #126
  }
}

\section{Version 1.14.0}{
  \itemize{
    \item option for uploading sorted taxon list
  }
}

\section{Version 1.12.6}{
  \itemize{
    \item fixed bug ordering gene IDs when using gene categories
  }
}

\section{Version 1.12.5}{
  \itemize{
    \item fixed bug multiple entries for one (super)taxon ID
  }
}

\section{Version 1.12.4}{
  \itemize{
    \item fixed bug download data
  }
}

\section{Version 1.12.3}{
  \itemize{
    \item fixed bug customized profile not showed
  }
}

\section{Version 1.12.1}{
  \itemize{
    \item added number of co-orthologs and number of taxa in each supertaxon
    \item replaced pfam link by interpro url
  }
}

\section{Version 1.10.3}{
  \itemize{
    \item fixed bug parsing taxon names for input with more than 9999 taxa
  }
}
 
\section{Version 1.10.1}{
  \itemize{
    \item fixed bug button for tree uploading disappear #119
    \item improved parsing seq ID to create links for external DB #117
    \item fixed bug grepping domains for group comparison fn
    \item fixed bug parsing data for a list of input gene IDs #122
  }
}

\section{Version 1.8.6}{
  \itemize{
    \item option to identify sequence source
  }
}

\section{Version 1.8.5}{
  \itemize{
    \item added functions for exporting plot settings
  }
}

\section{Version 1.8.4}{
  \itemize{
    \item fixed error reading taxonNamesReduced.txt that contains "#"
    \item added functions for import and export taxonomy DB
  }
}

\section{Version 1.8.3}{
  \itemize{
    \item fixed bug of group comparison function
  }
}

\section{Version 1.8.2}{
  \itemize{
    \item fixed loading cluster from config file
  }
}

\section{Version 1.8.1}{
  \itemize{
    \item do not show pfam links for smart domains and vice versa
  }
}

\section{Version 1.7.8}{
  \itemize{
    \item only mainInput is required in config file
  }
}

\section{Version 1.7.7}{
  \itemize{
    \item use config file for input files, refspec selection and othes settings
  }
}

\section{Version 1.6.6}{
  \itemize{
    \item turn off auto sizing for large number of taxa or genes (>= 10.000)
  }
}

\section{Version 1.6.5}{
  \itemize{
    \item fixed filter for "species relation"
    \item added midpoint colors
  }
}

\section{Version 1.6.2}{
  \itemize{
    \item increase default font size for profile and domain plot
    \item make links to DBs: ncbi taxonomy, ncbi protein, uniprot, pfam, smart
  }
}

\section{Version 1.6.1}{
  \itemize{
    \item modified taxonomy ranks (ropensci#875)
    \item improved rank indexing function (ropensci#874)
    \item improved x-axis label (#116)
  }
}

\section{Version 1.4.12}{
  \itemize{
    \item domain plot works with group ID containing pipe
  }
}

\section{Version 1.4.11}{
  \itemize{
    \item added check for invalid ids in newTaxa file
  }
}

\section{Version 1.4.10}{
  \itemize{
    \item fixed bug comparing unk taxon IDs with max ncbi taxID
  }
}

\section{Version 1.4.9}{
  \itemize{
    \item fixed bug comparing taxon IDs with max ncbi taxID
  }
}

\section{Version 1.4.8}{
  \itemize{
    \item fixed bug filterProfileData (some filtered data could not be plotted)
  }
}

\section{Version 1.4.5}{
  \itemize{
    \item Add auto sizing feature
  }
}

\section{Version 1.4.4}{
  \itemize{
    \item Fixed orthoxml parsing function
  }
}

\section{Version 1.4.3}{
  \itemize{
    \item Plot background for NA orthologs
    \item Fixed highlight by categories
  }
}

\section{Version 1.4.2}{
  \itemize{
    \item Fixed error when parsing large amount of new taxa
    \item Improved the speed of parsing new taxa
    \item Apply filter to refspec orthologs when not working with strain/species
  }
}
 
\section{Version 1.4.1}{
  \itemize{
    \item Fixed bug data lost after filtering var2
    \item Add filter data to detailed plot
  }
}

\section{Version 1.3.11}{
  \itemize{
    \item Add filter number of co-orthologs to parseInfoProfile()
  }
}

\section{Version 1.3.10}{
  \itemize{
    \item Calculate percentage of present taxa after filtering of var1 and var2
    \item Fixed filter when working with high taxonomy ranks
  }
}

\section{Version 1.2.8}{
  \itemize{
    \item Added new NCBI taxonomy ranks (e.g. biotype, isolate, pathogroup, ...)
    \item Added function to reset taxonomy data
  }
}

\section{Version 1.2.7}{
  \itemize{
    \item Solved problem with new NCBI taxonomy rank "clade" by replace them with "norank"
  }
}

\section{Version 1.2.6}{
  \itemize{
    \item Fixed bug customized profile of subset of taxa not clickable
  }
}

\section{Version 1.2.4}{
  \itemize{
    \item Fixed bug checking invalid taxon IDs
  }
}

\section{Version 1.2.1}{
  \itemize{
    \item Fixed bug in rankIndexing and processNcbiTaxonomy
    \item Improved check for invalid input taxon IDs
  }
}

\section{Version 1.1.12}{
  \itemize{
    \item Added pseudo IDs for Holozoa and Holomycota clades and their non-NCBI sub-clades
  }
}

\section{Version 1.1.11}{
  \itemize{
    \item Increased the resolution of the phylostratigraphy function
  }
}

\section{Version 1.1.10}{
  \itemize{
    \item Improved the rank indexing function
  }
}

\section{Version 1.1.6}{
  \itemize{
    \item Removed grDevices, grid, stats, utils from Imports list in DESCRIPTION
  }
}

\section{Version 1.1.5}{
  \itemize{
    \item Added progress indicators for data loading and processing steps
    \item Removed shinycssloaders
  }
}

\section{Version 1.1.3}{
  \itemize{
    \item Fixed bug listing taxa by selecting a supertaxon from a higher level
    \item Added message for downloading preprocessed data
  }
}

\section{Version 1.1.2}{
  \itemize{
    \item Fixed bug sorting taxa when taxonomy rank is set as strain
  }
}

\section{Version 1.1.1}{
  \itemize{
    \item Commented examples of OMA parser functions
    \item Turned off tests for OMA parser functions
  }
}

\section{Version 0.99.31}{
  \itemize{
    \item Submitted to Bioconductor
  }
}