%% BioMed_Central_Bib_Style_v1.01

\begin{thebibliography}{31}
% BibTex style file: bmc-mathphys.bst (version 2.1), 2014-07-24
\ifx \bisbn   \undefined \def \bisbn  #1{ISBN #1}\fi
\ifx \binits  \undefined \def \binits#1{#1}\fi
\ifx \bauthor  \undefined \def \bauthor#1{#1}\fi
\ifx \batitle  \undefined \def \batitle#1{#1}\fi
\ifx \bjtitle  \undefined \def \bjtitle#1{#1}\fi
\ifx \bvolume  \undefined \def \bvolume#1{\textbf{#1}}\fi
\ifx \byear  \undefined \def \byear#1{#1}\fi
\ifx \bissue  \undefined \def \bissue#1{#1}\fi
\ifx \bfpage  \undefined \def \bfpage#1{#1}\fi
\ifx \blpage  \undefined \def \blpage #1{#1}\fi
\ifx \burl  \undefined \def \burl#1{\textsf{#1}}\fi
\ifx \doiurl  \undefined \def \doiurl#1{\textsf{#1}}\fi
\ifx \betal  \undefined \def \betal{\textit{et al.}}\fi
\ifx \binstitute  \undefined \def \binstitute#1{#1}\fi
\ifx \binstitutionaled  \undefined \def \binstitutionaled#1{#1}\fi
\ifx \bctitle  \undefined \def \bctitle#1{#1}\fi
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\ifx \bpublisher  \undefined \def \bpublisher#1{#1}\fi
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\ifx \bseriesno  \undefined \def \bseriesno#1{#1}\fi
\ifx \blocation  \undefined \def \blocation#1{#1}\fi
\ifx \bsertitle  \undefined \def \bsertitle#1{#1}\fi
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\ifx \bsuffix \undefined \def \bsuffix#1{#1}\fi
\ifx \bparticle \undefined \def \bparticle#1{#1}\fi
\ifx \barticle \undefined \def \barticle#1{#1}\fi
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\ifx \url \undefined \def \url#1{\textsf{#1}}\fi
\ifx \bchapter \undefined \def \bchapter#1{#1}\fi
\ifx \bbook \undefined \def \bbook#1{#1}\fi
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\ifx \endbibitem  \undefined \def \endbibitem {}\fi
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\ifx \arxivurl  \undefined \def \arxivurl#1{\textsf{#1}}\fi
\csname PreBibitemsHook\endcsname

%%% 1
\bibitem{polyphen2}
\begin{barticle}
\bauthor{\bsnm{Adzhubei}, \binits{I.}},
\bauthor{\bsnm{Jordan}, \binits{D.M.}},
\bauthor{\bsnm{Sunyaev}, \binits{S.R.}}:
\batitle{{{P}redicting functional effect of human missense mutations using
  {P}oly{P}hen-2}}.
\bjtitle{Curr Protoc Hum Genet}
\bvolume{Chapter 7},
\bfpage{7}--\blpage{20}
(\byear{2013})
\end{barticle}
\endbibitem

%%% 2
\bibitem{soft:sift}
\begin{barticle}
\bauthor{\bsnm{Kumar}, \binits{P.}},
\bauthor{\bsnm{Henikoff}, \binits{S.}},
\bauthor{\bsnm{Ng}, \binits{P.C.}}:
\batitle{{P}redicting the effects of coding non-synonymous variants on protein
  function using the {S}{I}{F}{T} algorithm}.
\bjtitle{Nat Protoc}
\bvolume{4}(\bissue{7}),
\bfpage{1073}--\blpage{1081}
(\byear{2009})
\end{barticle}
\endbibitem

%%% 3
\bibitem{book:julie}
\begin{bbook}
\bauthor{\bsnm{Thompson}, \binits{J.D.}}:
\bbtitle{Statistics in Bioinformatics: Methods for Multiple Sequence
  Alignment}.
\bpublisher{Elsevier}, \blocation{???}
(\byear{2017})
\end{bbook}
\endbibitem

%%% 4
\bibitem{review:bawono}
\begin{barticle}
\bauthor{\bsnm{Bawono}, \binits{P.}},
\bauthor{\bsnm{Dijkstra}, \binits{M.}},
\bauthor{\bsnm{Pirovano}, \binits{W.}},
\bauthor{\bsnm{Feenstra}, \binits{A.}},
\bauthor{\bsnm{Abeln}, \binits{S.}},
\bauthor{\bsnm{Heringa}, \binits{J.}}:
\batitle{{{M}ultiple {S}equence {A}lignment}}.
\bjtitle{Methods Mol. Biol.}
\bvolume{1525},
\bfpage{167}--\blpage{189}
(\byear{2017})
\end{barticle}
\endbibitem

%%% 5
\bibitem{review:chatzou}
\begin{barticle}
\bauthor{\bsnm{Chatzou}, \binits{M.}},
\bauthor{\bsnm{Magis}, \binits{C.}},
\bauthor{\bsnm{Chang}, \binits{J.M.}},
\bauthor{\bsnm{Kemena}, \binits{C.}},
\bauthor{\bsnm{Bussotti}, \binits{G.}},
\bauthor{\bsnm{Erb}, \binits{I.}},
\bauthor{\bsnm{Notredame}, \binits{C.}}:
\batitle{{{M}ultiple sequence alignment modeling: methods and applications}}.
\bjtitle{Brief. Bioinformatics}
\bvolume{17}(\bissue{6}),
\bfpage{1009}--\blpage{1023}
(\byear{2016})
\end{barticle}
\endbibitem

%%% 6
\bibitem{soft:m2align}
\begin{barticle}
\bauthor{\bsnm{Zambrano-Vega}, \binits{C.}},
\bauthor{\bsnm{Nebro}, \binits{A.J.}},
\bauthor{\bsnm{Garcia-Nieto}, \binits{J.}},
\bauthor{\bsnm{Aldana-Montes}, \binits{J.F.}}:
\batitle{{{M}2{A}lign: parallel multiple sequence alignment with a
  multi-objective metaheuristic}}.
\bjtitle{Bioinformatics}
\bvolume{33}(\bissue{19}),
\bfpage{3011}--\blpage{3017}
(\byear{2017})
\end{barticle}
\endbibitem

%%% 7
\bibitem{listmsatools}
\begin{botherref}
List of alignments visualisation software.
\url{https://en.wikipedia.org/wiki/List\_of\_alignment\_visualization\_software}.
Accessed: 2017-08-14
\end{botherref}
\endbibitem

%%% 8
\bibitem{soft:jalview2}
\begin{barticle}
\bauthor{\bsnm{Waterhouse}, \binits{A.M.}},
\bauthor{\bsnm{Procter}, \binits{J.B.}},
\bauthor{\bsnm{Martin}, \binits{D.M.}},
\bauthor{\bsnm{Clamp}, \binits{M.}},
\bauthor{\bsnm{Barton}, \binits{G.J.}}:
\batitle{{{J}alview {V}ersion 2--a multiple sequence alignment editor and
  analysis workbench}}.
\bjtitle{Bioinformatics}
\bvolume{25}(\bissue{9}),
\bfpage{1189}--\blpage{1191}
(\byear{2009})
\end{barticle}
\endbibitem

%%% 9
\bibitem{soft:seqtools}
\begin{barticle}
\bauthor{\bsnm{Barson}, \binits{G.}},
\bauthor{\bsnm{Griffiths}, \binits{E.}}:
\batitle{{{S}eq{T}ools: visual tools for manual analysis of sequence
  alignments}}.
\bjtitle{BMC Res Notes}
\bvolume{9},
\bfpage{39}
(\byear{2016})
\end{barticle}
\endbibitem

%%% 10
\bibitem{soft:aliview}
\begin{barticle}
\bauthor{\bsnm{Larsson}, \binits{A.}}:
\batitle{{{A}li{V}iew: a fast and lightweight alignment viewer and editor for
  large datasets}}.
\bjtitle{Bioinformatics}
\bvolume{30}(\bissue{22}),
\bfpage{3276}--\blpage{3278}
(\byear{2014})
\end{barticle}
\endbibitem

%%% 11
\bibitem{soft:sqlite}
\begin{botherref}
\oauthor{\bsnm{Hipp}, \binits{D.R.}}:
SQLite home page.
\url{https://www.sqlite.org}.
Accessed: 2017-08-14
\end{botherref}
\endbibitem

%%% 12
\bibitem{soft:mafft}
\begin{barticle}
\bauthor{\bsnm{Katoh}, \binits{K.}},
\bauthor{\bsnm{Misawa}, \binits{K.}},
\bauthor{\bsnm{Kuma}, \binits{K.}},
\bauthor{\bsnm{Miyata}, \binits{T.}}:
\batitle{{{M}{A}{F}{F}{T}: a novel method for rapid multiple sequence alignment
  based on fast {F}ourier transform}}.
\bjtitle{Nucleic Acids Res.}
\bvolume{30}(\bissue{14}),
\bfpage{3059}--\blpage{3066}
(\byear{2002})
\end{barticle}
\endbibitem

%%% 13
\bibitem{soft:seqlab}
\begin{barticle}
\bauthor{\bsnm{Thompson}, \binits{S.M.}}:
\batitle{{{C}onstructing and refining multiple sequence alignments with
  {P}ile{U}p, {S}eq{L}ab, and the {G}{C}{G} suite}}.
\bjtitle{Curr Protoc Bioinformatics}
\bvolume{Chapter 3},
\bfpage{3}--\blpage{6}
(\byear{2003})
\end{barticle}
\endbibitem

%%% 14
\bibitem{soft:gcg}
\begin{barticle}
\bauthor{\bsnm{Womble}, \binits{D.D.}}:
\batitle{{{G}{C}{G}: {T}he {W}isconsin {P}ackage of sequence analysis
  programs}}.
\bjtitle{Methods Mol. Biol.}
\bvolume{132},
\bfpage{3}--\blpage{22}
(\byear{2000})
\end{barticle}
\endbibitem

%%% 15
\bibitem{soft:macsims}
\begin{barticle}
\bauthor{\bsnm{Thompson}, \binits{J.D.}},
\bauthor{\bsnm{Muller}, \binits{A.}},
\bauthor{\bsnm{Waterhouse}, \binits{A.}},
\bauthor{\bsnm{Procter}, \binits{J.}},
\bauthor{\bsnm{Barton}, \binits{G.J.}},
\bauthor{\bsnm{Plewniak}, \binits{F.}},
\bauthor{\bsnm{Poch}, \binits{O.}}:
\batitle{{{M}{A}{C}{S}{I}{M}{S}: multiple alignment of complete sequences
  information management system}}.
\bjtitle{BMC Bioinformatics}
\bvolume{7},
\bfpage{318}
(\byear{2006})
\end{barticle}
\endbibitem

%%% 16
\bibitem{soft:fastme}
\begin{barticle}
\bauthor{\bsnm{Lefort}, \binits{V.}},
\bauthor{\bsnm{Desper}, \binits{R.}},
\bauthor{\bsnm{Gascuel}, \binits{O.}}:
\batitle{{{F}ast{M}{E} 2.0: {A} {C}omprehensive, {A}ccurate, and {F}ast
  {D}istance-{B}ased {P}hylogeny {I}nference {P}rogram}}.
\bjtitle{Mol. Biol. Evol.}
\bvolume{32}(\bissue{10}),
\bfpage{2798}--\blpage{2800}
(\byear{2015})
\end{barticle}
\endbibitem

%%% 17
\bibitem{secator}
\begin{barticle}
\bauthor{\bsnm{Wicker}, \binits{N.}},
\bauthor{\bsnm{Perrin}, \binits{G.R.}},
\bauthor{\bsnm{Thierry}, \binits{J.C.}},
\bauthor{\bsnm{Poch}, \binits{O.}}:
\batitle{{{S}ecator: a program for inferring protein subfamilies from
  phylogenetic trees}}.
\bjtitle{Mol. Biol. Evol.}
\bvolume{18}(\bissue{8}),
\bfpage{1435}--\blpage{1441}
(\byear{2001})
\end{barticle}
\endbibitem

%%% 18
\bibitem{dpc}
\begin{barticle}
\bauthor{\bsnm{Wicker}, \binits{N.}},
\bauthor{\bsnm{Dembele}, \binits{D.}},
\bauthor{\bsnm{Raffelsberger}, \binits{W.}},
\bauthor{\bsnm{Poch}, \binits{O.}}:
\batitle{{{D}ensity of points clustering, application to transcriptomic data
  analysis}}.
\bjtitle{Nucleic Acids Res.}
\bvolume{30}(\bissue{18}),
\bfpage{3992}--\blpage{4000}
(\byear{2002})
\end{barticle}
\endbibitem

%%% 19
\bibitem{mixturemodel}
\begin{bbook}
\bauthor{\bsnm{McLachlan}, \binits{G.}},
\bauthor{\bsnm{Peel}, \binits{D.}}:
\bbtitle{Finite Mixture Models}.
\bpublisher{Wiley}, \blocation{???}
(\byear{2000})
\end{bbook}
\endbibitem

%%% 20
\bibitem{aic}
\begin{barticle}
\bauthor{\bsnm{Akaike}, \binits{H.}}:
\batitle{A new look at the statistical model identification}.
\bjtitle{IEEE Transactions on Automatic Control}
\bvolume{AC-19}(\bissue{6}),
\bfpage{716}--\blpage{723}
(\byear{1974})
\end{barticle}
\endbibitem

%%% 21
\bibitem{bic}
\begin{barticle}
\bauthor{\bsnm{Schwarz}, \binits{E.G.}}:
\batitle{Estimating the dimension of a model}.
\bjtitle{Annals of Statistics}
\bvolume{6}(\bissue{2}),
\bfpage{461}--\blpage{464}
(\byear{1978})
\end{barticle}
\endbibitem

%%% 22
\bibitem{valdar}
\begin{barticle}
\bauthor{\bsnm{Valdar}, \binits{W.S.}}:
\batitle{{{S}coring residue conservation}}.
\bjtitle{Proteins}
\bvolume{48}(\bissue{2}),
\bfpage{227}--\blpage{241}
(\byear{2002})
\end{barticle}
\endbibitem

%%% 23
\bibitem{johansson}
\begin{barticle}
\bauthor{\bsnm{Johansson}, \binits{F.}},
\bauthor{\bsnm{Toh}, \binits{H.}}:
\batitle{{{A} comparative study of conservation and variation scores}}.
\bjtitle{BMC Bioinformatics}
\bvolume{11},
\bfpage{388}
(\byear{2010})
\end{barticle}
\endbibitem

%%% 24
\bibitem{liu}
\begin{barticle}
\bauthor{\bsnm{Liu}, \binits{X.}},
\bauthor{\bsnm{Li}, \binits{J.}},
\bauthor{\bsnm{Guo}, \binits{W.}},
\bauthor{\bsnm{Wang}, \binits{W.}}:
\batitle{{{A} new method for quantifying residue conservation and its
  applications to the protein folding nucleus}}.
\bjtitle{Biochem. Biophys. Res. Commun.}
\bvolume{351}(\bissue{4}),
\bfpage{1031}--\blpage{1036}
(\byear{2006})
\end{barticle}
\endbibitem

%%% 25
\bibitem{liu2}
\begin{barticle}
\bauthor{\bsnm{Liu}, \binits{X.S.}},
\bauthor{\bsnm{Guo}, \binits{W.L.}}:
\batitle{{{R}obustness of the residue conservation score reflecting both
  frequencies and physicochemistries}}.
\bjtitle{Amino Acids}
\bvolume{34}(\bissue{4}),
\bfpage{643}--\blpage{652}
(\byear{2008})
\end{barticle}
\endbibitem

%%% 26
\bibitem{soft:clustalx}
\begin{barticle}
\bauthor{\bsnm{Thompson}, \binits{J.D.}},
\bauthor{\bsnm{Gibson}, \binits{T.J.}},
\bauthor{\bsnm{Plewniak}, \binits{F.}},
\bauthor{\bsnm{Jeanmougin}, \binits{F.}},
\bauthor{\bsnm{Higgins}, \binits{D.G.}}:
\batitle{{The CLUSTAL\_X windows interface: flexible strategies for multiple
  sequence alignment aided by quality analysis tools}}.
\bjtitle{Nucleic Acids Res.}
\bvolume{25}(\bissue{24}),
\bfpage{4876}--\blpage{4882}
(\byear{1997})
\end{barticle}
\endbibitem

%%% 27
\bibitem{bild}
\begin{barticle}
\bauthor{\bsnm{Altschul}, \binits{S.F.}},
\bauthor{\bsnm{Wootton}, \binits{J.C.}},
\bauthor{\bsnm{Zaslavsky}, \binits{E.}},
\bauthor{\bsnm{Yu}, \binits{Y.K.}}:
\batitle{{{T}he construction and use of log-odds substitution scores for
  multiple sequence alignment}}.
\bjtitle{PLoS Comput. Biol.}
\bvolume{6}(\bissue{7}),
\bfpage{1000852}
(\byear{2010})
\end{barticle}
\endbibitem

%%% 28
\bibitem{db:pdb}
\begin{botherref}
The RCSB Protein Data Bank.
\url{https://www.rcsb.org}.
Accessed: 2017-08-14
\end{botherref}
\endbibitem

%%% 29
\bibitem{db:uniprot}
\begin{barticle}
\bauthor{\bsnm{Pundir}, \binits{S.}},
\bauthor{\bsnm{Martin}, \binits{M.J.}},
\bauthor{\bsnm{O'Donovan}, \binits{C.}}:
\batitle{{{U}ni{P}rot {P}rotein {K}nowledgebase}}.
\bjtitle{Methods Mol. Biol.}
\bvolume{1558},
\bfpage{41}--\blpage{55}
(\byear{2017})
\end{barticle}
\endbibitem

%%% 30
\bibitem{db:refseq}
\begin{barticle}
\bauthor{\bsnm{Pundir}, \binits{S.}},
\bauthor{\bsnm{Martin}, \binits{M.J.}},
\bauthor{\bsnm{O'Donovan}, \binits{C.}}:
\batitle{{{U}ni{P}rot {P}rotein {K}nowledgebase}}.
\bjtitle{Methods Mol. Biol.}
\bvolume{1558},
\bfpage{41}--\blpage{55}
(\byear{2017})
\end{barticle}
\endbibitem

%%% 31
\bibitem{soft:tcltk}
\begin{botherref}
Tcl Developer's XChange.
\url{https://www.tcl.tk}.
Accessed: 2017-08-14
\end{botherref}
\endbibitem

\end{thebibliography}

\newcommand{\BMCxmlcomment}[1]{}

\BMCxmlcomment{

<refgrp>

<bibl id="B1">
  <title><p>{{P}redicting functional effect of human missense mutations using
  {P}oly{P}hen-2}</p></title>
  <aug>
    <au><snm>Adzhubei</snm><fnm>I.</fnm></au>
    <au><snm>Jordan</snm><fnm>D. M.</fnm></au>
    <au><snm>Sunyaev</snm><fnm>S. R.</fnm></au>
  </aug>
  <source>Curr Protoc Hum Genet</source>
  <pubdate>2013</pubdate>
  <volume>Chapter 7</volume>
  <fpage>Unit7.20</fpage>
</bibl>

<bibl id="B2">
  <title><p>{P}redicting the effects of coding non-synonymous variants on
  protein function using the {S}{I}{F}{T} algorithm</p></title>
  <aug>
    <au><snm>Kumar</snm><fnm>P.</fnm></au>
    <au><snm>Henikoff</snm><fnm>S.</fnm></au>
    <au><snm>Ng</snm><fnm>P. C.</fnm></au>
  </aug>
  <source>Nat Protoc</source>
  <pubdate>2009</pubdate>
  <volume>4</volume>
  <issue>7</issue>
  <fpage>1073</fpage>
  <lpage>-1081</lpage>
</bibl>

<bibl id="B3">
  <title><p>Statistics in bioinformatics: Methods for Multiple Sequence
  Alignment</p></title>
  <aug>
    <au><snm>Thompson</snm><fnm>J. D.</fnm></au>
  </aug>
  <publisher>Elsevier</publisher>
  <pubdate>2017</pubdate>
</bibl>

<bibl id="B4">
  <title><p>{{M}ultiple {S}equence {A}lignment}</p></title>
  <aug>
    <au><snm>Bawono</snm><fnm>P.</fnm></au>
    <au><snm>Dijkstra</snm><fnm>M.</fnm></au>
    <au><snm>Pirovano</snm><fnm>W.</fnm></au>
    <au><snm>Feenstra</snm><fnm>A.</fnm></au>
    <au><snm>Abeln</snm><fnm>S.</fnm></au>
    <au><snm>Heringa</snm><fnm>J.</fnm></au>
  </aug>
  <source>Methods Mol. Biol.</source>
  <pubdate>2017</pubdate>
  <volume>1525</volume>
  <fpage>167</fpage>
  <lpage>-189</lpage>
</bibl>

<bibl id="B5">
  <title><p>{{M}ultiple sequence alignment modeling: methods and
  applications}</p></title>
  <aug>
    <au><snm>Chatzou</snm><fnm>M.</fnm></au>
    <au><snm>Magis</snm><fnm>C.</fnm></au>
    <au><snm>Chang</snm><fnm>J. M.</fnm></au>
    <au><snm>Kemena</snm><fnm>C.</fnm></au>
    <au><snm>Bussotti</snm><fnm>G.</fnm></au>
    <au><snm>Erb</snm><fnm>I.</fnm></au>
    <au><snm>Notredame</snm><fnm>C.</fnm></au>
  </aug>
  <source>Brief. Bioinformatics</source>
  <pubdate>2016</pubdate>
  <volume>17</volume>
  <issue>6</issue>
  <fpage>1009</fpage>
  <lpage>-1023</lpage>
</bibl>

<bibl id="B6">
  <title><p>{{M}2{A}lign: parallel multiple sequence alignment with a
  multi-objective metaheuristic}</p></title>
  <aug>
    <au><snm>Zambrano Vega</snm><fnm>C.</fnm></au>
    <au><snm>Nebro</snm><fnm>A. J.</fnm></au>
    <au><snm>Garcia Nieto</snm><fnm>J.</fnm></au>
    <au><snm>Aldana Montes</snm><fnm>J. F.</fnm></au>
  </aug>
  <source>Bioinformatics</source>
  <pubdate>2017</pubdate>
  <volume>33</volume>
  <issue>19</issue>
  <fpage>3011</fpage>
  <lpage>-3017</lpage>
</bibl>

<bibl id="B7">
  <title><p>List of alignments visualisation software</p></title>
  <source>\url{https://en.wikipedia.org/wiki/List\_of\_alignment\_visualization\_software}</source>
  <note>Accessed: 2017-08-14</note>
</bibl>

<bibl id="B8">
  <title><p>{{J}alview {V}ersion 2--a multiple sequence alignment editor and
  analysis workbench}</p></title>
  <aug>
    <au><snm>Waterhouse</snm><fnm>A. M.</fnm></au>
    <au><snm>Procter</snm><fnm>J. B.</fnm></au>
    <au><snm>Martin</snm><fnm>D. M.</fnm></au>
    <au><snm>Clamp</snm><fnm>M.</fnm></au>
    <au><snm>Barton</snm><fnm>G. J.</fnm></au>
  </aug>
  <source>Bioinformatics</source>
  <pubdate>2009</pubdate>
  <volume>25</volume>
  <issue>9</issue>
  <fpage>1189</fpage>
  <lpage>-1191</lpage>
</bibl>

<bibl id="B9">
  <title><p>{{S}eq{T}ools: visual tools for manual analysis of sequence
  alignments}</p></title>
  <aug>
    <au><snm>Barson</snm><fnm>G.</fnm></au>
    <au><snm>Griffiths</snm><fnm>E.</fnm></au>
  </aug>
  <source>BMC Res Notes</source>
  <pubdate>2016</pubdate>
  <volume>9</volume>
  <fpage>39</fpage>
</bibl>

<bibl id="B10">
  <title><p>{{A}li{V}iew: a fast and lightweight alignment viewer and editor
  for large datasets}</p></title>
  <aug>
    <au><snm>Larsson</snm><fnm>A.</fnm></au>
  </aug>
  <source>Bioinformatics</source>
  <pubdate>2014</pubdate>
  <volume>30</volume>
  <issue>22</issue>
  <fpage>3276</fpage>
  <lpage>-3278</lpage>
</bibl>

<bibl id="B11">
  <title><p>SQLite home page</p></title>
  <aug>
    <au><snm>Hipp</snm><fnm>DR</fnm></au>
  </aug>
  <source>\url{https://www.sqlite.org}</source>
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</refgrp>
} % end of \BMCxmlcomment
