<s>
PHYLogeny	O
Inference	O
Package	O
(	O
PHYLIP	B-Application
)	O
is	O
a	O
free	O
computational	O
phylogenetics	O
package	O
of	O
programs	O
for	O
inferring	O
evolutionary	O
trees	O
(	O
phylogenies	O
)	O
.	O
</s>
<s>
It	O
consists	O
of	O
65	O
portable	O
programs	O
,	O
i.e.	O
,	O
the	O
source	O
code	O
is	O
written	O
in	O
the	O
programming	B-Language
language	I-Language
C	I-Language
.	O
As	O
of	O
version	O
3.696	O
,	O
it	O
is	O
licensed	O
as	O
open-source	B-Application
software	I-Application
;	O
versions	O
3.695	O
and	O
older	O
were	O
proprietary	B-Application
software	I-Application
freeware	B-License
.	O
</s>
<s>
Releases	O
occur	O
as	O
source	O
code	O
,	O
and	O
as	O
precompiled	O
executables	B-Application
for	O
many	O
operating	B-General_Concept
systems	I-General_Concept
including	O
Windows	B-Application
(	O
95	O
,	O
98	O
,	O
ME	O
,	O
NT	O
,	O
2000	O
,	O
XP	O
,	O
Vista	O
)	O
,	O
Mac	B-Operating_System
OS	I-Operating_System
8	I-Operating_System
,	O
Mac	B-Operating_System
OS	I-Operating_System
9	I-Operating_System
,	O
OS	B-Operating_System
X	I-Operating_System
,	O
Linux	B-Application
(	O
Debian	O
,	O
Red	O
Hat	O
)	O
;	O
and	O
FreeBSD	B-Operating_System
from	O
FreeBSD.org	O
.	O
</s>
<s>
The	O
programs	O
in	O
the	O
phylip	B-Application
package	O
were	O
written	O
by	O
Professor	O
Joseph	O
Felsenstein	O
,	O
of	O
the	O
Department	O
of	O
Genome	O
Sciences	O
and	O
the	O
Department	O
of	O
Biology	O
,	O
University	O
of	O
Washington	O
,	O
Seattle	O
.	O
</s>
<s>
The	O
data	O
is	O
read	O
into	O
the	O
program	O
from	O
a	O
text	O
file	O
,	O
which	O
the	O
user	O
can	O
prepare	O
using	O
any	O
word	O
processor	O
or	O
text	O
editor	O
(	O
but	O
this	O
text	O
file	O
cannot	O
be	O
in	O
the	O
special	O
format	O
of	O
the	O
word	O
processor	O
,	O
it	O
must	O
instead	O
be	O
in	O
flat	O
ASCII	B-Protocol
or	O
text	O
only	O
format	O
)	O
.	O
</s>
<s>
Some	O
sequence	O
analysis	O
programs	O
such	O
as	O
the	O
ClustalW	B-Application
alignment	O
program	O
can	O
write	O
data	O
files	O
in	O
the	O
PHYLIP	B-Application
format	O
.	O
</s>
<s>
If	O
the	O
phylip	B-Application
programs	O
do	O
not	O
find	O
this	O
file	O
,	O
they	O
then	O
ask	O
the	O
user	O
to	O
type	O
in	O
the	O
file	O
name	O
of	O
the	O
data	O
file	O
.	O
</s>
<s>
The	O
component	O
programs	O
of	O
phylip	B-Application
use	O
several	O
different	O
formats	O
,	O
all	O
of	O
which	O
are	O
relatively	O
simple	O
.	O
</s>
<s>
Names	O
are	O
limited	O
to	O
10	O
characters	O
by	O
default	O
and	O
must	O
be	O
blank-filled	O
to	O
be	O
of	O
that	O
length	O
and	O
followed	O
immediately	O
by	O
the	O
character	O
data	O
using	O
one-letter	O
codes	O
,	O
although	O
the	O
10	O
character	O
limit	O
name	O
can	O
be	O
changed	O
by	O
a	O
minor	O
modification	O
of	O
the	O
code	O
(	O
by	O
changing	O
nmlngth	O
in	O
phylip.h	O
and	O
recompiling	O
)	O
.	O
</s>
<s>
All	O
printable	O
ASCII/ISO	O
characters	O
are	O
allowed	O
names	O
,	O
except	O
for	O
parentheses	O
(	O
"	O
(	O
"	O
and	O
"	O
)	O
"	O
)	O
,	O
square	O
brackets	O
("["	O
and	O
"	O
]	O
"	O
)	O
,	O
colon	O
(	O
 "	O
:	O
"	O
)	O
,	O
semicolon	O
(";	O
"	O
)	O
and	O
comma	O
(","	O
)	O
.	O
</s>
<s>
Many	O
programs	O
for	O
phylogenetic	O
analyses	O
,	O
including	O
the	O
commonly-used	O
and	O
programs	O
,	O
use	O
the	O
phylip	B-Application
format	O
or	O
a	O
minor	O
modification	O
of	O
that	O
format	O
called	O
the	O
relaxed	O
phylip	B-Application
format	O
.	O
</s>
<s>
Relaxed	O
phylip	B-Application
format	O
(	O
sequential	O
)	O
:	O
</s>
<s>
The	O
primary	O
difference	O
in	O
relaxed	O
phylip	B-Application
format	O
is	O
the	O
absence	O
of	O
the	O
10	O
character	O
limit	O
and	O
the	O
removal	O
of	O
the	O
need	O
to	O
blank	O
fill	O
names	O
to	O
reach	O
that	O
length	O
(	O
although	O
filling	O
names	O
to	O
start	O
the	O
character	O
matrix	O
at	O
the	O
same	O
position	O
can	O
improve	O
readability	O
for	O
user	O
)	O
.	O
</s>
<s>
Like	O
strict	O
phylip	B-Application
format	O
files	O
,	O
relaxed	O
phylip	B-Application
format	O
files	O
can	O
be	O
in	O
interleaved	O
format	O
and	O
include	O
spaces	O
and	O
endlines	O
within	O
the	O
sequence	O
data	O
.	O
</s>
<s>
The	O
programs	O
that	O
use	O
distance	O
data	O
,	O
like	O
the	O
neighbor	O
program	O
that	O
implements	O
the	O
neighbor-joining	B-Algorithm
method	O
,	O
also	O
use	O
a	O
simple	O
distance	O
matrix	O
format	O
the	O
includes	O
only	O
the	O
number	O
of	O
taxa	O
,	O
their	O
names	O
,	O
and	O
numerical	O
values	O
for	O
the	O
distances	O
:	O
</s>
<s>
Phylip	B-Application
distance	O
matrix	O
:	O
</s>
<s>
Programs	O
that	O
use	O
trees	O
as	O
input	O
accept	O
the	O
trees	O
in	O
Newick	B-Data_Structure
format	I-Data_Structure
,	O
an	O
informal	O
standard	O
agreed	O
to	O
in	O
1986	O
by	O
authors	O
of	O
seven	O
major	O
phylogeny	O
packages	O
.	O
</s>
<s>
Trees	O
written	O
onto	O
outtree	O
are	O
in	O
the	O
Newick	B-Data_Structure
format	I-Data_Structure
.	O
</s>
<s>
+Programs	O
listed	O
in	O
PHYLIP	B-Application
Program	O
name	O
Description	O
protpars	O
Estimates	O
phylogenies	O
of	O
peptide	O
sequences	O
using	O
the	O
parsimony	O
method	O
dnapars	O
Estimates	O
phylogenies	O
of	O
DNA	O
sequences	O
using	O
the	O
parsimony	O
method	O
dnapenny	O
DNA	O
parsimony	O
branch	O
and	O
bound	O
method	O
,	O
finds	O
all	O
of	O
the	O
most	O
parsimonious	O
phylogenies	O
for	O
nucleic	O
acid	O
sequences	O
by	O
branch-and-bound	O
search	O
dnamove	O
Interactive	O
construction	O
of	O
phylogenies	O
from	O
nucleic	O
acid	O
sequences	O
,	O
with	O
their	O
evaluation	O
by	O
DNA	O
parsimony	O
method	O
,	O
with	O
compatibility	O
and	O
display	O
of	O
reconstructed	O
ancestral	O
bases	O
dnacomp	O
Estimates	O
phylogenies	O
from	O
nucleic	O
acid	O
sequence	O
data	O
using	O
the	O
compatibility	O
criterion	O
dnaml	O
Estimates	O
phylogenies	O
from	O
nucleotide	O
sequences	O
using	O
the	O
maximum	O
likelihood	O
method	O
dnamlk	O
DNA	O
maximum	O
likelihood	O
method	O
with	O
molecular	O
clock	O
;	O
using	O
both	O
dnaml	O
and	O
dnamlk	O
together	O
permits	O
a	O
likelihood-ratio	B-General_Concept
test	I-General_Concept
for	O
the	O
molecular	O
clock	O
hypothesis	O
proml	O
Estimates	O
phylogenies	O
from	O
protein	O
amino	O
acid	O
sequences	O
by	O
using	O
the	O
maximum	O
likelihood	O
method	O
promlk	O
Protein	O
sequence	O
maximum	O
likelihood	O
method	O
with	O
molecular	O
clock	O
restml	O
Estimation	O
of	O
phylogenies	O
by	O
maximum	O
likelihood	O
using	O
restriction	O
sites	O
data	O
;	O
not	O
from	O
restriction	O
fragments	O
but	O
from	O
the	O
presence	O
or	O
absence	O
of	O
individual	O
sites	O
dnainvar	O
For	O
nucleic	O
acid	O
sequence	O
data	O
on	O
four	O
species	O
,	O
computes	O
Lake	O
's	O
and	O
Cavender	O
's	O
phylogenetic	O
invariants	O
,	O
which	O
test	O
alternative	O
tree	O
topologies	O
dnadist	O
DNA	O
distance	O
method	O
which	O
computes	O
four	O
different	O
distances	O
between	O
species	O
from	O
nucleic	O
acid	O
sequences	O
;	O
distances	O
can	O
then	O
be	O
used	O
in	O
the	O
distance	O
matrix	O
programs	O
protdist	O
Protein	O
sequence	O
distance	O
method	O
which	O
computes	O
a	O
distance	O
measure	O
for	O
sequences	O
,	O
using	O
maximum	O
likelihood	O
estimates	O
based	O
on	O
the	O
Dayhoff	O
PAM	O
matrix	O
,	O
Kimura	O
's	O
1983	O
approximation	O
to	O
it	O
,	O
or	O
a	O
model	O
based	O
on	O
genetic	O
code	O
plus	O
a	O
constraint	O
on	O
changing	O
to	O
a	O
different	O
category	O
of	O
amino	O
acid	O
restdist	O
Distances	O
calculated	O
from	O
restriction	O
sites	O
data	O
or	O
restriction	O
fragments	O
data	O
seqboot	O
Bootstrapping-jackknifing	O
program	O
;	O
reads	O
in	O
a	O
data	B-General_Concept
set	I-General_Concept
,	O
and	O
emits	O
multiple	O
data	B-General_Concept
sets	I-General_Concept
from	O
it	O
by	O
bootstrap	O
resampling	O
fitch	O
Fitch-Margoliash	O
distance	O
matrix	O
method	O
;	O
estimates	O
phylogenies	O
from	O
distance	O
matrix	O
data	O
under	O
the	O
additive	O
tree	O
model	O
according	O
to	O
which	O
the	O
distances	O
are	O
expected	O
to	O
equal	O
the	O
sums	O
of	O
branch	O
lengths	O
between	O
species	O
kitsch	O
Fitch-Margoliash	O
distance	O
matrix	O
method	O
with	O
molecular	O
clock	O
;	O
estimates	O
phylogenies	O
from	O
distance	O
matrix	O
data	O
under	O
the	O
ultrametric	O
model	O
which	O
is	O
the	O
same	O
as	O
the	O
additive	O
tree	O
model	O
except	O
an	O
evolutionary	O
clock	O
is	O
assumed	O
neighbor	O
Implementation	O
of	O
the	O
methods	O
neighbor	B-Algorithm
joining	I-Algorithm
and	O
UPGMA	B-Algorithm
contml	O
Maximum	O
likelihood	O
continuous	O
characters	O
and	O
gene	O
frequencies	O
;	O
estimates	O
phylogenies	O
from	O
gene	O
frequency	O
data	O
by	O
maximum	O
likelihood	O
under	O
a	O
model	O
in	O
which	O
all	O
divergence	O
is	O
due	O
to	O
genetic	O
drift	O
in	O
the	O
absence	O
of	O
new	O
mutations	O
;	O
also	O
does	O
maximum	O
likelihood	O
analysis	O
of	O
continuous	O
characters	O
that	O
evolve	O
by	O
a	O
Brownian	O
Motion	O
model	O
,	O
assuming	O
that	O
the	O
characters	O
evolve	O
at	O
equal	O
rates	O
and	O
in	O
an	O
uncorrelated	O
fashion	O
;	O
does	O
not	O
account	O
for	O
character	O
correlations	O
contrast	O
Reads	O
a	O
tree	O
from	O
a	O
tree	O
file	O
,	O
and	O
a	O
data	B-General_Concept
set	I-General_Concept
with	O
continuous	O
characters	O
data	O
,	O
and	O
emits	O
the	O
independent	O
contrasts	O
for	O
those	O
characters	O
,	O
for	O
use	O
in	O
any	O
multivariate	O
statistics	O
package	O
gendist	O
Genetic	O
distance	O
program	O
which	O
computes	O
one	O
of	O
three	O
different	O
genetic	O
distance	O
formulas	O
from	O
gene	O
frequency	O
data	O
pars	O
Unordered	O
multistate	O
discrete-characters	O
parsimony	O
method	O
mix	O
Estimates	O
phylogenies	O
by	O
some	O
parsimony	O
methods	O
for	O
discrete	O
character	O
data	O
with	O
two	O
states	O
(	O
0	O
,	O
1	O
)	O
;	O
allows	O
using	O
methods	O
:	O
Wagner	O
,	O
Camin-Sokal	O
,	O
or	O
arbitrary	O
mixes	O
penny	O
Branch	O
and	O
bound	O
mixed	O
method	O
which	O
finds	O
all	O
of	O
the	O
most	O
parsimonious	O
phylogenies	O
for	O
discrete-character	O
data	O
with	O
two	O
states	O
,	O
for	O
the	O
Wagner	O
,	O
Camin-Sokal	O
,	O
and	O
mixed	O
parsimony	O
criteria	O
using	O
the	O
branch-and-bound	O
method	O
of	O
exact	O
search	O
move	O
Interactive	O
construction	O
of	O
phylogenies	O
from	O
discrete	O
character	O
data	O
with	O
two	O
states	O
(	O
0	O
,	O
1	O
)	O
;	O
evaluates	O
parsimony	O
and	O
compatibility	O
criteria	O
for	O
those	O
phylogenies	O
and	O
displays	O
reconstructed	O
states	O
throughout	O
the	O
tree	O
dollop	O
Estimates	O
phylogenies	O
by	O
the	O
Dollo	O
or	O
polymorphism	O
parsimony	O
criteria	O
for	O
discrete	O
character	O
data	O
with	O
two	O
states	O
(	O
0	O
,	O
1	O
)	O
dolpenny	O
Finds	O
all	O
or	O
most	O
parsimonious	O
phylogenies	O
for	O
discrete-character	O
data	O
with	O
two	O
states	O
,	O
for	O
the	O
Dollo	O
or	O
polymorphism	O
parsimony	O
criteria	O
using	O
the	O
branch-and-bound	O
method	O
of	O
exact	O
search	O
dolmove	O
Interactive	O
construction	O
of	O
phylogenies	O
from	O
discrete	O
character	O
data	O
with	O
two	O
states	O
(	O
0	O
,	O
1	O
)	O
using	O
the	O
Dollo	O
or	O
polymorphism	O
parsimony	O
criteria	O
;	O
evaluates	O
parsimony	O
and	O
compatibility	O
criteria	O
for	O
those	O
phylogenies	O
;	O
displays	O
reconstructed	O
states	O
throughout	O
the	O
tree	O
clique	O
Finds	O
the	O
largest	O
clique	O
of	O
mutually	O
compatible	O
characters	O
,	O
and	O
the	O
phylogeny	O
which	O
they	O
recommend	O
,	O
for	O
discrete	O
character	O
data	O
with	O
two	O
states	O
(	O
0	O
,	O
1	O
)	O
;	O
the	O
largest	O
clique	O
(	O
or	O
all	O
cliques	O
within	O
a	O
given	O
size	O
range	O
of	O
the	O
largest	O
one	O
)	O
are	O
found	O
by	O
a	O
fast	O
branch	O
and	O
bound	O
search	O
method	O
factor	O
Character	O
recoding	O
program	O
which	O
takes	O
discrete	O
multistate	O
data	O
with	O
character	O
state	O
trees	O
and	O
emits	O
the	O
corresponding	O
data	B-General_Concept
set	I-General_Concept
with	O
two	O
states	O
(	O
0	O
,	O
1	O
)	O
drawgram	O
Rooted	O
tree	O
drawing	O
program	O
which	O
plots	O
rooted	O
phylogenies	O
,	O
cladograms	O
,	O
and	O
phenograms	O
in	O
a	O
wide	O
variety	O
of	O
user-controllable	O
formats	O
.	O
</s>
<s>
Many	O
programs	O
that	O
convert	O
among	O
alignment	O
formats	O
will	O
output	O
data	O
in	O
phylip	B-Application
or	O
relaxed	O
phylip	B-Application
format	O
.	O
</s>
<s>
For	O
example	O
,	O
conversion	O
between	O
the	O
PHYLIP	B-Application
multiple	O
sequence	O
alignment	O
format	O
and	O
Multi-FASTA	O
format	O
can	O
done	O
with	O
Genozip	O
using	O
genocat	O
--fasta	O
or	O
genocat	O
--phylip	O
.	O
</s>
<s>
The	O
PAUP*	B-Application
software	O
package	O
is	O
especially	O
useful	O
for	O
converting	O
between	O
the	O
Nexus	O
format	O
and	O
phylip	B-Application
format	O
.	O
</s>
