[29]. The tool is integrated into the HaMStR package (https://
github.com/BIONF/HaMStR).
2.4.4 DoMosaics [30] DoMosaics (http://www.domosaics.net/) is a tool to annotate and
visualize protein domain architectures in protein sequences. The
resulting architectures can be displayed on a user-provided phylog-
eny of the analyzed sequences to reconstruct domain architecture
evolution over time.
2.5 Evolutionary
Sequence Analysis
2.5.1 HMMER [31]
The HMMER package (http://hmmer.org/) is a collection of tools
for the analysis of biological sequences using profile hidden Markov
models. HMMER is often used together with a profile database,
such as Pfam or many of the databases that participate in InterPro
(http://www.ebi.ac.uk/interpro/).2.5.2 MUSCLE [32] MUSCLE is a multiple sequence alignment tool that is available
both as a web server (http://www.ebi.ac.uk/Tools/msa/muscle/)
and as a stand-alone tool (http://www.drive5.com/muscle/
downloads.htm).
2.5.3 MAFFT [33] The web server for the multiple sequence alignment tool MAFFT is
available athttp://mafft.cbrc.jp/alignment/server/and as a stand-
alone tool for download athttp://mafft.cbrc.jp/alignment/soft
ware/.
2.5.4 ProtTest [34] ProtTest (http://darwin.uvigo.es/software/prottest_server.html)
facilitates the selection of best-fitting amino acid substitution
model for protein sequence evolution.
2.5.5 RAxML [35] RAxML (http://sco.h-its.org/exelixis/web/software/raxml/
index.html) is a maximum likelihood tree reconstruction method.
2.6 Visualization
of Phylogenetic Trees
2.6.1 FigTree [36]
FigTree (http://tree.bio.ed.ac.uk/software/figtree/) is a graphical
tree visualization software and provides tools to output high-
resolution publication-ready tree images.2.6.2 Baobab Baobab (http://kimura.univ-montp2.fr/~jdutheil/Baobab/Bao
bab.html) is a JAVA-based tree visualization software and allows
interactive tree manipulation.
2.7 Visualization
of Phylogenetic
Profiles
The PhyloProfile application (https://github.com/BIONF/
PhyloProfile) is a R/Shiny package to dynamically visualize and
explore phylogenetic profiles.2.8 Taxonomic
Databases
The NCBI taxonomy (https://www.ncbi.nlm.nih.gov/taxonomy)
is a curated classification and nomenclature for all of the organisms
in the public sequence databases.116 Arpit Jain et al.