Bioperl Tree Object

joshuapk · 03-12-2013, 07:35 AM

If anyone uses Bioperl Tree module out there I could use your help. I am finding that when I read in a .dnd file (newick) from a clustal alignment. Then count the number of nodes that exist within the tree it is far too large. For instance in the following tree:
(
(
(
(
NP_777373.1:0.10091,
YP_003212822.1:0.09142)
:0.15908,
(
(
(
(
YP_873922.1:0.03218,
NP_777370.1:0.02792)
:0.00092,
NP_066255.1:0.03525)
:0.01017,
YP_002004564.1:0.04619)
:0.18566,
NP_783196.1:0.22090)
:0.01501)
:0.13384,
(
(
(
YP_164336.1:0.03270,
YP_022762.1:0.03183)
:0.16070,
YP_077278.1:0.19536)
:0.10230,
NP_051035.1:0.30447)
:0.06925)
:0.01514,
(
(
(
YP_002364399.1:0.06202,
NP_062875.1:0.06149)
:0.04748,
NP_068828.1:0.10606)
:0.27052,
(
(
NP_663315.1:0.01634,
YP_213937.1:0.01805)
:0.01563,
YP_529550.1:0.03414)
:0.34412)
:0.00909,
(
YP_002905325.1:0.40730,
(
NP_056820.1:0.27798,
YP_720001.1:0.27151)
:0.11890)
:0.05569);

There should only be 18 nodes. Though the Bioperl module has found 38 for some reason.
Thanks

joshuapk · 03-12-2013, 07:44 AM

I lied, I wasn't counting the leaves as nodes.
Thanks

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03-12-2013, 07:35 AM	#1
joshuapk Junior Member Location: Pittsburgh Join Date: Mar 2012 Posts: 9	Bioperl Tree Object If anyone uses Bioperl Tree module out there I could use your help. I am finding that when I read in a .dnd file (newick) from a clustal alignment. Then count the number of nodes that exist within the tree it is far too large. For instance in the following tree: ( ( ( ( NP_777373.1:0.10091, YP_003212822.1:0.09142) :0.15908, ( ( ( ( YP_873922.1:0.03218, NP_777370.1:0.02792) :0.00092, NP_066255.1:0.03525) :0.01017, YP_002004564.1:0.04619) :0.18566, NP_783196.1:0.22090) :0.01501) :0.13384, ( ( ( YP_164336.1:0.03270, YP_022762.1:0.03183) :0.16070, YP_077278.1:0.19536) :0.10230, NP_051035.1:0.30447) :0.06925) :0.01514, ( ( ( YP_002364399.1:0.06202, NP_062875.1:0.06149) :0.04748, NP_068828.1:0.10606) :0.27052, ( ( NP_663315.1:0.01634, YP_213937.1:0.01805) :0.01563, YP_529550.1:0.03414) :0.34412) :0.00909, ( YP_002905325.1:0.40730, ( NP_056820.1:0.27798, YP_720001.1:0.27151) :0.11890) :0.05569); There should only be 18 nodes. Though the Bioperl module has found 38 for some reason. Thanks

03-12-2013, 07:44 AM	#2
joshuapk Junior Member Location: Pittsburgh Join Date: Mar 2012 Posts: 9	I lied, I wasn't counting the leaves as nodes. Thanks