<s>
XRATE	B-Application
is	O
a	O
program	O
for	O
prototyping	O
phylogenetic	O
hidden	O
Markov	O
models	O
and	O
stochastic	B-General_Concept
context-free	I-General_Concept
grammars	I-General_Concept
.	O
</s>
<s>
It	O
is	O
used	O
to	O
discover	O
patterns	O
of	O
evolutionary	O
conservation	O
in	O
sequence	B-Algorithm
alignments	I-Algorithm
.	O
</s>
<s>
As	O
an	O
example	O
of	O
how	O
XRATE	B-Application
is	O
used	O
,	O
consider	O
a	O
protein-coding	O
gene	O
consisting	O
of	O
exons	O
interspersed	O
with	O
introns	O
.	O
</s>
<s>
XRATE	B-Application
allows	O
the	O
user	O
to	O
specify	O
such	O
models	O
in	O
a	O
configuration	O
file	O
and	O
estimate	O
their	O
parameters	O
(	O
evolutionary	O
rates	O
,	O
length	O
distributions	O
of	O
exons	O
and	O
introns	O
,	O
etc	O
.	O
)	O
</s>
<s>
directly	O
from	O
alignment	O
data	O
,	O
using	O
the	O
Expectation-maximization	B-Algorithm
algorithm	I-Algorithm
.	O
</s>
<s>
XRATE	B-Application
can	O
be	O
downloaded	O
as	O
part	O
of	O
the	O
.	O
</s>
