<s>
BAli-Phy	B-Application
is	O
a	O
free	O
software	O
program	O
for	O
simultaneously	O
estimating	O
a	O
multiple	O
sequence	O
alignment	O
and	O
its	O
phylogenetic	O
tree	O
.	O
</s>
<s>
BAli-Phy	B-Application
achieves	O
high	O
accuracy	O
in	O
alignment	O
estimation	O
by	O
using	O
information	O
from	O
the	O
co-estimated	O
phylogeny	O
.	O
</s>
<s>
BAli-Phy	B-Application
takes	O
alignment	O
uncertainty	O
into	O
account	O
while	O
estimating	O
the	O
phylogeny	O
by	O
averaging	O
over	O
possible	O
alignments	O
.	O
</s>
<s>
BAli-Phy	B-Application
produces	O
a	O
Bayesian	O
posterior	O
distribution	O
on	O
both	O
the	O
alignments	O
and	O
the	O
tree	O
.	O
</s>
<s>
BAli-Phy	B-Application
uses	O
Markov	B-General_Concept
chain	I-General_Concept
Monte	I-General_Concept
Carlo	I-General_Concept
methods	I-General_Concept
for	O
estimation	O
.	O
</s>
<s>
BAli-Phy	B-Application
can	O
handle	O
both	O
near-optimal	O
alignment	O
uncertainty	O
and	O
evolutionary	O
parameter	O
uncertainty	O
by	O
integrating	O
over	O
possible	O
alignments	O
and	O
parameter	O
values	O
.	O
</s>
<s>
BAli-Phy	B-Application
accepts	O
nucleotide	O
,	O
amino	O
acid	O
,	O
and	O
codon	O
sequences	O
in	O
FASTA	O
format	O
.	O
</s>
<s>
Trees	O
are	O
output	O
in	O
Newick	B-Data_Structure
format	I-Data_Structure
.	O
</s>
