<s>
Mesquite	B-Application
is	O
a	O
software	O
package	O
primarily	O
designed	O
for	O
phylogenetic	O
analyses	O
.	O
</s>
<s>
Mesquite	B-Application
is	O
largely	O
written	O
in	O
Java	B-Language
and	O
uses	O
NEXUS-formatted	O
files	O
as	O
input	O
.	O
</s>
<s>
Mesquite	B-Application
is	O
available	O
as	O
a	O
compiled	O
executable	O
for	O
Macintosh	O
,	O
Windows	O
,	O
and	O
Unix-like	B-Operating_System
platforms	O
,	O
and	O
the	O
source	O
code	O
is	O
available	O
on	O
GitHub	B-Application
.	O
</s>
<s>
The	O
architecture	O
of	O
Mesquite	B-Application
was	O
explicitly	O
designed	O
to	O
exploit	O
the	O
modularity	O
and	O
extensibility	O
of	O
Object-oriented	B-Language
programming	I-Language
.	O
</s>
<s>
In	O
practice	O
,	O
Mesquite	B-Application
modules	O
are	O
Java	B-Language
classes	O
,	O
usually	O
concrete	O
sub-classes	O
of	O
abstract	O
class	O
definitions	O
.	O
</s>
<s>
This	O
modular	O
architecture	O
has	O
afforded	O
the	O
development	O
of	O
additional	O
packages	O
that	O
can	O
be	O
used	O
as	O
plug-ins	O
to	O
Mesquite	B-Application
.	O
</s>
<s>
Mesquite	B-Application
provides	O
a	O
number	O
of	O
analyses	O
including	O
ancestral	O
state	O
estimation	O
and	O
diversification	O
analysis	O
.	O
</s>
<s>
Mesquite	B-Application
also	O
contains	O
tools	O
for	O
simulating	O
data	O
such	O
as	O
species	O
trees	O
,	O
gene	O
trees	O
,	O
and	O
DNA	O
matrices	O
.	O
</s>
<s>
The	O
base	O
distribution	O
of	O
Mesquite	B-Application
affords	O
interoperability	O
with	O
other	O
programs	O
,	O
for	O
such	O
purposes	O
as	O
multiple	O
sequence	O
alignment	O
(	O
e.g.	O
</s>
<s>
Clustal	B-Application
and	O
MAFFT	B-Application
)	O
,	O
as	O
well	O
as	O
the	O
ability	O
to	O
retrieve	O
DNA	O
sequence	O
data	O
from	O
GenBank	O
.	O
</s>
<s>
Mesquite	B-Application
includes	O
some	O
rudimentary	O
tools	O
for	O
phylogenetic	O
tree	O
estimation	O
;	O
however	O
,	O
the	O
Zephyr	O
package	O
provides	O
a	O
Mesquite	B-Application
interface	O
for	O
interacting	O
with	O
other	O
phylogenetic	O
inference	O
programs	O
including	O
RAxML	O
,	O
PAUP*	B-Application
,	O
and	O
GARLI	O
.	O
</s>
