biopython (python3) phylo, how does the distance function works?
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Using the Phylo package in Python3, I am trying to compute distances between two terminal nodes (leaves) of a neighbour-joining tree. To do this, the package implements a distance function. However, the distance function gives me a different result from what is in my newick file (the difference is very light but quite important in my work). Here is my code:
#Libraries
import os
from Bio import Phylo
from io import StringIO
# Tree
handleD = StringIO("((E:0.2,D:0.1,C:0.1,B:0.3)2:0.3,A:0.5)1;")
treeD = Phylo.read(handleD,"newick")
# Distance
treeD.distance("E","D")
The distance returns 0.30000000000000004 and not 0.3 as describe in the newick format.
I tried to look at the source code: http://biopython.org/DIST/docs/api/Bio.Phylo.BaseTree.TreeMixin-class.html#distance
that leads to that function : http://biopython.org/DIST/docs/api/Bio.Nexus.Trees-pysrc.html#Tree.sum_branchlength
but it doesn't explain why there is a difference in the values.
Have you got an explanation why the function returns 0.30000000000000004 instead of 0.3 as described in the newick format?
Thanks in advance.
biopython
asked Nov 26 '18 at 16:47
SamAlnSamAln
11
add a comment |
Using the Phylo package in Python3, I am trying to compute distances between two terminal nodes (leaves) of a neighbour-joining tree. To do this, the package implements a distance function. However, the distance function gives me a different result from what is in my newick file (the difference is very light but quite important in my work). Here is my code:
#Libraries
import os
from Bio import Phylo
from io import StringIO
# Tree
handleD = StringIO("((E:0.2,D:0.1,C:0.1,B:0.3)2:0.3,A:0.5)1;")
treeD = Phylo.read(handleD,"newick")
# Distance
treeD.distance("E","D")
The distance returns 0.30000000000000004 and not 0.3 as describe in the newick format.
I tried to look at the source code: http://biopython.org/DIST/docs/api/Bio.Phylo.BaseTree.TreeMixin-class.html#distance
that leads to that function : http://biopython.org/DIST/docs/api/Bio.Nexus.Trees-pysrc.html#Tree.sum_branchlength
but it doesn't explain why there is a difference in the values.
Have you got an explanation why the function returns 0.30000000000000004 instead of 0.3 as described in the newick format?
Thanks in advance.
biopython
asked Nov 26 '18 at 16:47
SamAlnSamAln
11
stackoverflow.com/questions/588004/…
– Chris_Rands
Nov 28 '18 at 13:08
Indeed ! Thank you
– SamAln
Nov 29 '18 at 14:21
Possible duplicate of Is floating point math broken?
– Chris_Rands
Nov 29 '18 at 14:58
And some python specific read on this: docs.python.org/3/tutorial/floatingpoint.html
– Hielke Walinga
Dec 9 '18 at 16:43
add a comment |
Using the Phylo package in Python3, I am trying to compute distances between two terminal nodes (leaves) of a neighbour-joining tree. To do this, the package implements a distance function. However, the distance function gives me a different result from what is in my newick file (the difference is very light but quite important in my work). Here is my code:
#Libraries
import os
from Bio import Phylo
from io import StringIO
# Tree
handleD = StringIO("((E:0.2,D:0.1,C:0.1,B:0.3)2:0.3,A:0.5)1;")
treeD = Phylo.read(handleD,"newick")
# Distance
treeD.distance("E","D")
The distance returns 0.30000000000000004 and not 0.3 as describe in the newick format.
I tried to look at the source code: http://biopython.org/DIST/docs/api/Bio.Phylo.BaseTree.TreeMixin-class.html#distance
that leads to that function : http://biopython.org/DIST/docs/api/Bio.Nexus.Trees-pysrc.html#Tree.sum_branchlength
but it doesn't explain why there is a difference in the values.
Have you got an explanation why the function returns 0.30000000000000004 instead of 0.3 as described in the newick format?
Thanks in advance.
biopython
asked Nov 26 '18 at 16:47
SamAlnSamAln
11
Using the Phylo package in Python3, I am trying to compute distances between two terminal nodes (leaves) of a neighbour-joining tree. To do this, the package implements a distance function. However, the distance function gives me a different result from what is in my newick file (the difference is very light but quite important in my work). Here is my code:
#Libraries
import os
from Bio import Phylo
from io import StringIO
# Tree
handleD = StringIO("((E:0.2,D:0.1,C:0.1,B:0.3)2:0.3,A:0.5)1;")
treeD = Phylo.read(handleD,"newick")
# Distance
treeD.distance("E","D")
The distance returns 0.30000000000000004 and not 0.3 as describe in the newick format.
I tried to look at the source code: http://biopython.org/DIST/docs/api/Bio.Phylo.BaseTree.TreeMixin-class.html#distance
that leads to that function : http://biopython.org/DIST/docs/api/Bio.Nexus.Trees-pysrc.html#Tree.sum_branchlength
but it doesn't explain why there is a difference in the values.
Have you got an explanation why the function returns 0.30000000000000004 instead of 0.3 as described in the newick format?
Thanks in advance.
biopython
biopython
asked Nov 26 '18 at 16:47
SamAlnSamAln
11
asked Nov 26 '18 at 16:47
SamAlnSamAln
11
asked Nov 26 '18 at 16:47
SamAlnSamAln
11
asked Nov 26 '18 at 16:47
SamAlnSamAln
11
asked Nov 26 '18 at 16:47
SamAlnSamAln
11
11
stackoverflow.com/questions/588004/…
– Chris_Rands
Nov 28 '18 at 13:08
Indeed ! Thank you
– SamAln
Nov 29 '18 at 14:21
Possible duplicate of Is floating point math broken?
– Chris_Rands
Nov 29 '18 at 14:58
And some python specific read on this: docs.python.org/3/tutorial/floatingpoint.html
– Hielke Walinga
Dec 9 '18 at 16:43
add a comment |
stackoverflow.com/questions/588004/…
– Chris_Rands
Nov 28 '18 at 13:08
Indeed ! Thank you
– SamAln
Nov 29 '18 at 14:21
Possible duplicate of Is floating point math broken?
– Chris_Rands
Nov 29 '18 at 14:58
And some python specific read on this: docs.python.org/3/tutorial/floatingpoint.html
– Hielke Walinga
Dec 9 '18 at 16:43
stackoverflow.com/questions/588004/…
– Chris_Rands
Nov 28 '18 at 13:08
stackoverflow.com/questions/588004/…
– Chris_Rands
Nov 28 '18 at 13:08
Indeed ! Thank you
– SamAln
Nov 29 '18 at 14:21
Indeed ! Thank you
– SamAln
Nov 29 '18 at 14:21
Possible duplicate of Is floating point math broken?
– Chris_Rands
Nov 29 '18 at 14:58
Possible duplicate of Is floating point math broken?
– Chris_Rands
Nov 29 '18 at 14:58
And some python specific read on this: docs.python.org/3/tutorial/floatingpoint.html
– Hielke Walinga
Dec 9 '18 at 16:43
And some python specific read on this: docs.python.org/3/tutorial/floatingpoint.html
– Hielke Walinga
Dec 9 '18 at 16:43
add a comment |
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stackoverflow.com/questions/588004/…
– Chris_Rands
Nov 28 '18 at 13:08
Indeed ! Thank you
– SamAln
Nov 29 '18 at 14:21
Possible duplicate of Is floating point math broken?
– Chris_Rands
Nov 29 '18 at 14:58
And some python specific read on this: docs.python.org/3/tutorial/floatingpoint.html
– Hielke Walinga
Dec 9 '18 at 16:43