<s>
T-REX	B-Application
(	O
Tree	O
and	O
Reticulogram	O
Reconstruction	O
)	O
is	O
a	O
freely	O
available	O
web	B-Application
server	I-Application
,	O
developed	O
at	O
the	O
department	O
of	O
Computer	O
Science	O
of	O
the	O
Université	O
du	O
Québec	O
à	O
Montréal	O
,	O
dedicated	O
to	O
the	O
inference	O
,	O
validation	O
and	O
visualization	O
of	O
phylogenetic	O
trees	O
and	O
phylogenetic	O
networks	O
.	O
</s>
<s>
The	O
T-REX	B-Application
web	B-Application
server	I-Application
allows	O
the	O
users	O
to	O
perform	O
several	O
popular	O
methods	O
of	O
phylogenetic	O
analysis	O
as	O
well	O
as	O
some	O
new	O
phylogenetic	O
applications	O
for	O
inferring	O
,	O
drawing	O
and	O
validating	O
phylogenetic	O
trees	O
and	O
networks	O
.	O
</s>
<s>
The	O
following	O
methods	O
for	O
inferring	O
and	O
validating	O
phylogenetic	O
trees	O
using	O
distances	O
are	O
available	O
:	O
Neighbor	B-Algorithm
joining	I-Algorithm
(	O
NJ	O
)	O
,	O
,	O
,	O
UNJ	O
,	O
ADDTREE	O
,	O
MW	O
,	O
FITCH	O
and	O
Circular	O
order	O
reconstruction	O
.	O
</s>
<s>
For	O
the	O
maximum	O
parsimony	O
:	O
DNAPARS	O
,	O
PROTPARS	O
,	O
PARS	O
and	O
DOLLOP	O
,	O
all	O
of	O
them	O
from	O
the	O
PHYLIP	B-Application
package	O
,	O
and	O
for	O
the	O
maximum	O
likelihood	O
:	O
PhyML	O
,	O
RAxML	O
,	O
DNAML	O
,	O
DNAMLK	O
,	O
PROML	O
and	O
PROMLK	O
,	O
the	O
four	O
latter	O
methods	O
are	O
from	O
the	O
PHYLIP	B-Application
package	O
,	O
are	O
available	O
.	O
</s>
<s>
Input	O
data	O
can	O
be	O
in	O
the	O
three	O
following	O
formats	O
:	O
Newick	B-Data_Structure
format	I-Data_Structure
,	O
PHYLIP	B-Application
and	O
FASTA	O
format	O
.	O
</s>
<s>
All	O
graphical	O
results	O
provided	O
by	O
the	O
T-REX	B-Application
server	O
can	O
be	O
saved	O
in	O
the	O
SVG	O
(	O
Scalable	O
Vector	O
Graphics	O
)	O
format	O
and	O
then	O
opened	O
and	O
modified	O
(	O
e.g.	O
</s>
<s>
A	O
developed	O
application	O
for	O
drawing	O
phylogenetic	O
trees	O
allowing	O
for	O
saving	O
them	O
in	O
the	O
Newick	B-Data_Structure
format	I-Data_Structure
.	O
</s>
<s>
Complete	O
and	O
partial	O
Horizontal	O
gene	O
transfer	O
detection	O
and	O
validation	O
methods	O
are	O
included	O
in	O
the	O
T-REX	B-Application
server	O
.	O
</s>
<s>
The	O
web	B-Application
server	I-Application
version	O
of	O
T-REX	B-Application
also	O
provides	O
the	O
possibility	O
of	O
inferring	O
the	O
supporting	O
tree	O
from	O
one	O
distance	O
matrix	O
and	O
then	O
for	O
adding	O
reticulation	O
branches	O
using	O
another	O
distance	O
matrix	O
.	O
</s>
<s>
MAFFT	B-Application
,	O
MUSCLE	O
(	O
alignment	O
software	O
)	O
and	O
ClustalW	B-Application
,	O
which	O
are	O
among	O
the	O
most	O
widely	O
used	O
multiple	O
sequence	O
alignment	O
tools	O
,	O
are	O
available	O
with	O
slow	O
and	O
fast	O
pairwise	O
alignment	O
options	O
.	O
</s>
<s>
The	O
following	O
popular	O
substitution	O
models	O
of	O
DNA	O
and	O
amino	O
acids	O
evolution	O
,	O
allowing	O
for	O
estimating	O
evolutionary	O
distances	O
from	O
sequence	O
data	O
,	O
have	O
been	O
included	O
to	O
T-REX	B-Application
:	O
Uncorrected	O
distance	O
,	O
Jukes-Cantor	O
(	O
Jukes	O
and	O
Cantor	O
1969	O
)	O
,	O
K80	O
–	O
2	O
parameters	O
(	O
Kimura	O
1980	O
)	O
,	O
T92	O
(	O
Tamura	O
1992	O
)	O
,	O
Tajima-Nei	O
(	O
Tajima	O
and	O
Nei	O
1984	O
)	O
,	O
Jin-Nei	O
gamma	O
(	O
Jin	O
and	O
Nei	O
1990	O
)	O
,	O
Kimura	O
protein	O
(	O
Kimura	O
1983	O
)	O
,	O
LogDet	O
(	O
Lockhart	O
et	O
al	O
.	O
</s>
<s>
This	O
program	O
computes	O
the	O
Robinson	B-Algorithm
–	I-Algorithm
Foulds	I-Algorithm
metric	I-Algorithm
(	O
RF	O
)	O
topological	O
distance	O
(	O
Robinson	O
and	O
Foulds	O
1981	O
)	O
,	O
which	O
is	O
a	O
popular	O
measure	O
of	O
the	O
trees	O
similarity	O
,	O
between	O
the	O
first	O
tree	O
and	O
all	O
the	O
following	O
trees	O
specified	O
by	O
the	O
user	O
.	O
</s>
<s>
Newick	O
to	O
Distance	O
matrix	O
and	O
Distance	O
matrix	O
to	O
Newick	B-Data_Structure
format	I-Data_Structure
conversion	O
.	O
</s>
<s>
An	O
in-house	O
application	O
allows	O
the	O
user	O
to	O
convert	O
a	O
phylogenetic	O
tree	O
from	O
the	O
Newick	B-Data_Structure
format	I-Data_Structure
to	O
the	O
Distance	O
matrix	O
format	O
and	O
vice	O
versa	O
.	O
</s>
