<s>
A	O
cladogram	B-Application
(	O
from	O
Greek	O
clados	O
"	O
branch	O
"	O
and	O
gramma	O
"	O
character	O
"	O
)	O
is	O
a	O
diagram	O
used	O
in	O
cladistics	O
to	O
show	O
relations	O
among	O
organisms	O
.	O
</s>
<s>
A	O
cladogram	B-Application
is	O
not	O
,	O
however	O
,	O
an	O
evolutionary	O
tree	O
because	O
it	O
does	O
not	O
show	O
how	O
ancestors	O
are	O
related	O
to	O
descendants	O
,	O
nor	O
does	O
it	O
show	O
how	O
much	O
they	O
have	O
changed	O
,	O
so	O
many	O
differing	O
evolutionary	O
trees	O
can	O
be	O
consistent	O
with	O
the	O
same	O
cladogram	B-Application
.	O
</s>
<s>
A	O
cladogram	B-Application
uses	O
lines	O
that	O
branch	O
off	O
in	O
different	O
directions	O
ending	O
at	O
a	O
clade	O
,	O
a	O
group	O
of	O
organisms	O
with	O
a	O
last	O
common	O
ancestor	O
.	O
</s>
<s>
There	O
are	O
many	O
shapes	O
of	O
cladograms	B-Application
but	O
they	O
all	O
have	O
lines	O
that	O
branch	O
off	O
from	O
other	O
lines	O
.	O
</s>
<s>
Although	O
traditionally	O
such	O
cladograms	B-Application
were	O
generated	O
largely	O
on	O
the	O
basis	O
of	O
morphological	O
characters	O
,	O
DNA	O
and	O
RNA	O
sequencing	O
data	O
and	O
computational	O
phylogenetics	O
are	O
now	O
very	O
commonly	O
used	O
in	O
the	O
generation	O
of	O
cladograms	B-Application
,	O
either	O
on	O
their	O
own	O
or	O
in	O
combination	O
with	O
morphology	O
.	O
</s>
<s>
The	O
characteristics	O
used	O
to	O
create	O
a	O
cladogram	B-Application
can	O
be	O
roughly	O
categorized	O
as	O
either	O
morphological	O
(	O
synapsid	O
skull	O
,	O
warm	O
blooded	O
,	O
notochord	O
,	O
unicellular	O
,	O
etc	O
.	O
)	O
</s>
<s>
However	O
,	O
homoplasy	O
is	O
often	O
not	O
evident	O
from	O
inspection	O
of	O
the	O
character	O
itself	O
(	O
as	O
in	O
DNA	O
sequence	O
,	O
for	O
example	O
)	O
,	O
and	O
is	O
then	O
detected	O
by	O
its	O
incongruence	O
(	O
unparsimonious	O
distribution	O
)	O
on	O
a	O
most-parsimonious	O
cladogram	B-Application
.	O
</s>
<s>
Although	O
the	O
wings	O
of	O
birds	O
,	O
bats	B-Application
,	O
and	O
insects	O
serve	O
the	O
same	O
function	O
,	O
each	O
evolved	O
independently	O
,	O
as	O
can	O
be	O
seen	O
by	O
their	O
anatomy	O
.	O
</s>
<s>
If	O
a	O
bird	O
,	O
bat	B-Application
,	O
and	O
a	O
winged	O
insect	O
were	O
scored	O
for	O
the	O
character	O
,	O
"	O
presence	O
of	O
wings	O
"	O
,	O
a	O
homoplasy	O
would	O
be	O
introduced	O
into	O
the	O
dataset	O
,	O
and	O
this	O
could	O
potentially	O
confound	O
the	O
analysis	O
,	O
possibly	O
resulting	O
in	O
a	O
false	O
hypothesis	O
of	O
relationships	O
.	O
</s>
<s>
A	O
cladogram	B-Application
is	O
the	O
diagrammatic	O
result	O
of	O
an	O
analysis	O
,	O
which	O
groups	O
taxa	O
on	O
the	O
basis	O
of	O
synapomorphies	O
alone	O
.	O
</s>
<s>
There	O
are	O
many	O
other	O
phylogenetic	O
algorithms	O
that	O
treat	O
data	O
somewhat	O
differently	O
,	O
and	O
result	O
in	O
phylogenetic	O
trees	O
that	O
look	O
like	O
cladograms	B-Application
but	O
are	O
not	O
cladograms	B-Application
.	O
</s>
<s>
For	O
example	O
,	O
phenetic	O
algorithms	O
,	O
such	O
as	O
UPGMA	O
and	O
Neighbor-Joining	B-Algorithm
,	O
group	O
by	O
overall	O
similarity	O
,	O
and	O
treat	O
both	O
synapomorphies	O
and	O
symplesiomorphies	O
as	O
evidence	O
of	O
grouping	O
,	O
The	O
resulting	O
diagrams	O
are	O
phenograms	O
,	O
not	O
cladograms	B-Application
,	O
Similarly	O
,	O
the	O
results	O
of	O
model-based	O
methods	O
(	O
Maximum	O
Likelihood	O
or	O
Bayesian	O
approaches	O
)	O
that	O
take	O
into	O
account	O
both	O
branching	O
order	O
and	O
"	O
branch	O
length	O
,	O
"	O
count	O
both	O
synapomorphies	O
and	O
autapomorphies	O
as	O
evidence	O
for	O
or	O
against	O
grouping	O
,	O
The	O
diagrams	O
resulting	O
from	O
those	O
sorts	O
of	O
analysis	O
are	O
not	O
cladograms	B-Application
,	O
either	O
.	O
</s>
<s>
There	O
are	O
several	O
algorithms	O
available	O
to	O
identify	O
the	O
"	O
best	O
"	O
cladogram	B-Application
.	O
</s>
<s>
Most	O
algorithms	O
use	O
a	O
metric	O
to	O
measure	O
how	O
consistent	O
a	O
candidate	O
cladogram	B-Application
is	O
with	O
the	O
data	O
.	O
</s>
<s>
Most	O
cladogram	B-Application
algorithms	O
use	O
the	O
mathematical	O
techniques	O
of	O
optimization	O
and	O
minimization	O
.	O
</s>
<s>
In	O
general	O
,	O
cladogram	B-Application
generation	O
algorithms	O
must	O
be	O
implemented	O
as	O
computer	O
programs	O
,	O
although	O
some	O
algorithms	O
can	O
be	O
performed	O
manually	O
when	O
the	O
data	O
sets	O
are	O
modest	O
(	O
for	O
example	O
,	O
just	O
a	O
few	O
species	O
and	O
a	O
couple	O
of	O
characteristics	O
)	O
.	O
</s>
<s>
Algorithms	O
for	O
cladograms	B-Application
or	O
other	O
types	O
of	O
phylogenetic	O
trees	O
include	O
least	B-Algorithm
squares	I-Algorithm
,	O
neighbor-joining	B-Algorithm
,	O
parsimony	O
,	O
maximum	O
likelihood	O
,	O
and	O
Bayesian	O
inference	O
.	O
</s>
<s>
Biologists	O
sometimes	O
use	O
the	O
term	O
parsimony	O
for	O
a	O
specific	O
kind	O
of	O
cladogram	B-Application
generation	O
algorithm	O
and	O
sometimes	O
as	O
an	O
umbrella	O
term	O
for	O
all	O
phylogenetic	O
algorithms	O
.	O
</s>
<s>
Algorithms	O
that	O
perform	O
optimization	O
tasks	O
(	O
such	O
as	O
building	O
cladograms	B-Application
)	O
can	O
be	O
sensitive	O
to	O
the	O
order	O
in	O
which	O
the	O
input	O
data	O
(	O
the	O
list	O
of	O
species	O
and	O
their	O
characteristics	O
)	O
is	O
presented	O
.	O
</s>
<s>
Inputting	O
the	O
data	O
in	O
various	O
orders	O
can	O
cause	O
the	O
same	O
algorithm	O
to	O
produce	O
different	O
"	O
best	O
"	O
cladograms	B-Application
.	O
</s>
<s>
Using	O
different	O
algorithms	O
on	O
a	O
single	O
data	O
set	O
can	O
sometimes	O
yield	O
different	O
"	O
best	O
"	O
cladograms	B-Application
,	O
because	O
each	O
algorithm	O
may	O
have	O
a	O
unique	O
definition	O
of	O
what	O
is	O
"	O
best	O
"	O
.	O
</s>
<s>
Because	O
of	O
the	O
astronomical	O
number	O
of	O
possible	O
cladograms	B-Application
,	O
algorithms	O
cannot	O
guarantee	O
that	O
the	O
solution	O
is	O
the	O
overall	O
best	O
solution	O
.	O
</s>
<s>
A	O
nonoptimal	O
cladogram	B-Application
will	O
be	O
selected	O
if	O
the	O
program	O
settles	O
on	O
a	O
local	O
minimum	O
rather	O
than	O
the	O
desired	O
global	O
minimum	O
.	O
</s>
<s>
To	O
help	O
solve	O
this	O
problem	O
,	O
many	O
cladogram	B-Application
algorithms	O
use	O
a	O
simulated	B-Algorithm
annealing	I-Algorithm
approach	O
to	O
increase	O
the	O
likelihood	O
that	O
the	O
selected	O
cladogram	B-Application
is	O
the	O
optimal	O
one	O
.	O
</s>
<s>
The	O
basal	O
position	O
is	O
the	O
direction	O
of	O
the	O
base	O
(	O
or	O
root	O
)	O
of	O
a	O
rooted	O
phylogenetic	O
tree	O
or	O
cladogram	B-Application
.	O
</s>
<s>
The	O
incongruence	B-Application
length	I-Application
difference	I-Application
test	I-Application
(	O
ILD	O
)	O
is	O
a	O
measurement	O
of	O
how	O
the	O
combination	O
of	O
different	O
datasets	O
(	O
e.g.	O
</s>
<s>
The	O
consistency	B-Application
index	I-Application
(	O
CI	O
)	O
measures	O
the	O
consistency	O
of	O
a	O
tree	O
to	O
a	O
set	O
of	O
data	O
–	O
a	O
measure	O
of	O
the	O
minimum	O
amount	O
of	O
homoplasy	O
implied	O
by	O
the	O
tree	O
.	O
</s>
<s>
It	O
is	O
calculated	O
by	O
counting	O
the	O
minimum	O
number	O
of	O
changes	O
in	O
a	O
dataset	O
and	O
dividing	O
it	O
by	O
the	O
actual	O
number	O
of	O
changes	O
needed	O
for	O
the	O
cladogram	B-Application
.	O
</s>
<s>
A	O
consistency	B-Application
index	I-Application
can	O
also	O
be	O
calculated	O
for	O
an	O
individual	O
character	O
i	O
,	O
denoted	O
ci	O
.	O
</s>
<s>
The	O
rescaled	O
consistency	B-Application
index	I-Application
(	O
RC	O
)	O
is	O
obtained	O
by	O
multiplying	O
the	O
CI	O
by	O
the	O
RI	O
;	O
in	O
effect	O
this	O
stretches	O
the	O
range	O
of	O
the	O
CI	O
such	O
that	O
its	O
minimum	O
theoretically	O
attainable	O
value	O
is	O
rescaled	O
to	O
0	O
,	O
with	O
its	O
maximum	O
remaining	O
at	O
1	O
.	O
</s>
