2.3.2 OMA [23] OMA (http://omabrowser.org/oma/home/) is a comprehensive
database providing access to precomputed orthologs on different
levels of inclusiveness. Orthologs between pairs of species—similar
to the InParanoid orthologs—are the most inclusive level. They are
complemented by hierarchical orthologous groups (HOGs) com-
prising sequences from more than two species. OMA groups, the
most stringent level, represent cliques of orthologs for which the
algorithm confirmed orthology between any pair of proteins in the
group. A stand-alone version for OMA is available athttp://
omabrowser.org/standalone/.
2.3.3 OrthoDB [24] OrthoDB is a comprehensive catalog of orthologous sequences
across the tree of life. OrthoDB provides hierarchal orthologs for
each major clade of the taxonomy. OrthoDB provides ready-to-
download, precomputed orthologs for extant protein sequences
(http://www.orthodb.org/). The stand-alone version for the soft-
ware is available athttp://www.orthodb.org/?page¼software.
2.3.4 HaMStR [25] The HaMStR package is a collection of tools to identify and anno-
tate orthologs in collections of protein or transcript sequences.
HaMStR [25] is a profile hidden Markov model (pHMM)-based
method to extend predefined orthologous groups with sequences
from further species. HaMStR-OneSeq [26] is an extension of the
HaMStR algorithm for a targeted ortholog search starting with
single seed sequences. FAS-S is a software for annotating and
scoring feature architecture similarity between pairs of sequences.
The HaMStR package is available athttps://github.com/BIONF/
HaMStR.
2.4 Software
for Domain
Architecture Analysis
and Comparison
2.4.1 InterProScan [27]
InterProScan annotates a query protein for the presence of protein
domains, protein family classification, and other features. Inter-
ProScan is available both as a web server (http://www.ebi.ac.uk/
Tools/pfa/iprscan5/) and as a stand-alone tool (ftp://ftp.ebi.ac.
uk/pub/software/unix/iprscan/5/).2.4.2 Pfam Database
[28]
Pfam (http://pfam.xfam.org/) is a large database comprising mul-
tiple sequence alignments (MSAs) and hidden Markov models
(HMMs) of protein domains and families. The Pfam web server
facilitates an online annotation of protein domains. Alternatively,
the Pfam database can be downloaded for stand-alone usage, e.g.,
in combination with the HMMER package (seeSubheading2.5).2.4.3 FAS-S The Feature Architecture Similarity Score, FAS-S, is a stand-alone
program to compare feature architecture between two protein
sequences. Features here refer to protein domains, secondary struc-
ture elements, and low-complexity regions. The similarity scoring is
based on an algorithm originally implemented into FACT
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