<s>
HYPHY	B-Application
(	O
)	O
is	O
a	O
free	O
multiplatform	O
(	O
Mac	O
,	O
Windows	O
and	O
UNIX	O
)	O
computational	O
phylogenetics	O
software	O
package	O
intended	O
to	O
perform	O
maximum	O
likelihood	O
analyses	O
of	O
genetic	O
sequence	O
data	O
and	O
equipped	O
with	O
tools	O
to	O
test	O
various	O
statistical	O
hypotheses	O
.	O
</s>
<s>
The	O
HYPHY	B-Application
name	O
is	O
an	O
abbreviation	O
for	O
"	O
HYpothesis	O
testing	O
using	O
PHYlogenies	O
"	O
.	O
</s>
<s>
As	O
of	O
March	O
2018	O
,	O
about	O
2,000	O
peer-reviewed	O
scientific	O
journal	O
articles	O
cite	O
HYPHY	B-Application
.	O
</s>
<s>
HYPHY	B-Application
supports	O
analysis	O
of	O
nucleotide	O
,	O
protein	O
and	O
codon	O
sequences	O
,	O
using	O
predefined	O
standard	O
models	O
or	O
user-defined	O
models	O
of	O
evolution	O
.	O
</s>
<s>
HyPhy	B-Application
includes	O
a	O
versatile	O
suite	O
of	O
methods	O
to	O
detect	O
adaptive	O
evolution	O
at	O
individual	O
amino-acid	O
sites	O
and/or	O
lineages	O
,	O
including	O
generalizations	O
of	O
Nielsen-Yang	O
PAML	O
and	O
Suzuki-Gojobori	O
approaches	O
and	O
many	O
others	O
.	O
</s>
<s>
The	O
development	O
of	O
HyPhy	B-Application
started	O
in	O
1997	O
,	O
with	O
the	O
first	O
public	O
release	O
in	O
2000	O
and	O
the	O
most	O
recent	O
version	O
as	O
of	O
December	O
2020	O
being	O
2.5	O
.	O
</s>
<s>
HYPHY	B-Application
is	O
distributed	O
as	O
freeware	O
with	O
source	O
code	O
released	O
under	O
the	B-License
MIT	I-License
License	I-License
.	O
</s>
<s>
The	O
source	O
code	O
is	O
available	O
so	O
that	O
users	O
can	O
compile	O
the	O
HyPhy	B-Application
application	O
on	O
POSIX	O
systems	O
.	O
</s>
<s>
A	O
subset	O
of	O
HYPHY	B-Application
methods	O
for	O
detecting	O
adaptive	O
evolution	O
are	O
also	O
made	O
available	O
by	O
the	O
HYPHY	B-Application
team	O
at	O
Temple	O
University	O
on	O
the	O
cluster	O
.	O
</s>
