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Max Telford
,
Rutger Vos
4
11/13/18
Collapse each internal node of a tree in turn and print out tree
Would it be possible to generate names for the internal nodes a priori? Names should be copied over
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Collapse each internal node of a tree in turn and print out tree
Would it be possible to generate names for the internal nodes a priori? Names should be copied over
11/13/18
Lee Katz
2
8/11/16
comparison to Phylip
I noticed finally that I was getting random results sometimes and so I looked around for what the
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comparison to Phylip
I noticed finally that I was getting random results sometimes and so I looked around for what the
8/11/16
Erik Hanschen
,
Rutger Vos
2
6/8/16
'keep' function?
Hi Erik, there isn't a problem with your code, there is a problem with our implementation, which
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'keep' function?
Hi Erik, there isn't a problem with your code, there is a problem with our implementation, which
6/8/16
Ashish Jain
,
Rutger Vos
6
9/9/15
How to scale up the branch length of a phylogenetic tree using Phylo.draw() function
Sorry for this post. This is for biopython group. Regards, Ashish Jain On Wednesday, 9 September 2015
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How to scale up the branch length of a phylogenetic tree using Phylo.draw() function
Sorry for this post. This is for biopython group. Regards, Ashish Jain On Wednesday, 9 September 2015
9/9/15
Fabian Schreiber
, …
Rutger Vos
6
4/16/15
Newick -> Phyloxml -> add Annotations
Hi Li, sorry about the slow response! If you still need this, it should be pretty easy to do - do you
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Newick -> Phyloxml -> add Annotations
Hi Li, sorry about the slow response! If you still need this, it should be pretty easy to do - do you
4/16/15
willingtone odhiambo
,
Rutger Vos
8
11/5/14
BIO::PHYLO TREE GENERATOR AND IO
Hi Willingtone, the error message indicates that the module Math::Random is not installed on your
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BIO::PHYLO TREE GENERATOR AND IO
Hi Willingtone, the error message indicates that the module Math::Random is not installed on your
11/5/14
Yan Wong
,
Rutger Vos
4
7/10/14
to_newick(-nodelabels=>1) generates "fake" nodenames
Hi Yan, sorry about the slow response. I have altered the behaviour of to_newick a bit because I was
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to_newick(-nodelabels=>1) generates "fake" nodenames
Hi Yan, sorry about the slow response. I have altered the behaviour of to_newick a bit because I was
7/10/14
Yan Wong
,
Rutger Vos
5
6/30/14
escaped quotes in newick filenames
On Monday, 30 June 2014 09:15:04 UTC+1, Rutger Vos wrote: Mmmm.... well, Bio::Phylo doesn't
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escaped quotes in newick filenames
On Monday, 30 June 2014 09:15:04 UTC+1, Rutger Vos wrote: Mmmm.... well, Bio::Phylo doesn't
6/30/14
Yan Wong
,
Rutger Vos
7
6/27/14
Comments with newlines at start of newick file
On Friday, 27 June 2014 13:41:40 UTC+1, Rutger Vos wrote: You could also in a separate block slurp
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Comments with newlines at start of newick file
On Friday, 27 June 2014 13:41:40 UTC+1, Rutger Vos wrote: You could also in a separate block slurp
6/27/14
Yan Wong
,
Rutger Vos
3
6/27/14
Two more issues
On Friday, 27 June 2014 09:57:52 UTC+1, Rutger Vos wrote: ... you install the latest development
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Two more issues
On Friday, 27 June 2014 09:57:52 UTC+1, Rutger Vos wrote: ... you install the latest development
6/27/14
Yan Wong
,
Rutger Vos
3
6/26/14
Adding branch lengths
On Thursday, 26 June 2014 13:15:26 UTC+1, Rutger Vos wrote: $tree->visit(... Ah, tat's what I
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Adding branch lengths
On Thursday, 26 June 2014 13:15:26 UTC+1, Rutger Vos wrote: $tree->visit(... Ah, tat's what I
6/26/14
Yan Wong
,
Rutger Vos
5
6/26/14
Simplifying and extracting large trees
On Thursday, 26 June 2014 13:13:33 UTC+1, Rutger Vos wrote: Hope this helps, Thanks of the reply. By
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Simplifying and extracting large trees
On Thursday, 26 June 2014 13:13:33 UTC+1, Rutger Vos wrote: Hope this helps, Thanks of the reply. By
6/26/14
Ivan Adzhubey
4/29/14
Ancestral state reconstruction?
Hi, I have an alignment (FASTA) and a tree (Newick). Is there any way to reconstruct states for all (
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Ancestral state reconstruction?
Hi, I have an alignment (FASTA) and a tree (Newick). Is there any way to reconstruct states for all (
4/29/14
Joe
,
Rutger Vos
3
2/7/14
get_cherries() missing cherries? -- trying to get all bipartitions
Hi Rutger, Thanks for your response. I guess get_entities suffers from the same bug. My end goal is
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get_cherries() missing cherries? -- trying to get all bipartitions
Hi Rutger, Thanks for your response. I guess get_entities suffers from the same bug. My end goal is
2/7/14
Wongsapat Tangwanidgoon
,
Rutger Vos
2
1/7/13
Q&A
Make Phylogenetictree
Dear Wongsapat, I assume that your input is a character state matrix, out of which you want to infer
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Q&A
Make Phylogenetictree
Dear Wongsapat, I assume that your input is a character state matrix, out of which you want to infer
1/7/13
László Nagy
,
Rutger Vos
3
10/11/12
rerooting trees - set_root_node
Hi Rutger, thanks, this helps, now it is working. cheers, Laszlo On Thursday, October 11, 2012 11:20:
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rerooting trees - set_root_node
Hi Rutger, thanks, this helps, now it is working. cheers, Laszlo On Thursday, October 11, 2012 11:20:
10/11/12
Rutger Vos
10/11/12
Re: Bio::Phylo - calculate branch lengths for certain taxa?
Dear Evan, > I'm writing to find out if what I am currently trying to do is possible in >
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Re: Bio::Phylo - calculate branch lengths for certain taxa?
Dear Evan, > I'm writing to find out if what I am currently trying to do is possible in >
10/11/12
László Nagy
,
Rutger Vos
2
10/11/12
Re: Abridged summary of bio-phylo@googlegroups.com - 1 Message in 1 Topic
Hi Laszlo, firstly, let me apologize for being so slow to respond - the last few weeks have been
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Re: Abridged summary of bio-phylo@googlegroups.com - 1 Message in 1 Topic
Hi Laszlo, firstly, let me apologize for being so slow to respond - the last few weeks have been
10/11/12
László Nagy
9/24/12
Re: Abridged summary of bio-phylo@googlegroups.com - 3 Messages in 2 Topics
Hi Rutger, thanks for the hint with the insert() function. I figured I will have to use the
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Re: Abridged summary of bio-phylo@googlegroups.com - 3 Messages in 2 Topics
Hi Rutger, thanks for the hint with the insert() function. I figured I will have to use the
9/24/12
László Nagy
,
Rutger Vos
2
9/13/12
Re: Abridged summary of bio-phylo@googlegroups.com - 1 Message in 1 Topic
Hi László, if you add a matrix row that is longer than the current nchar, more characters will be
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Re: Abridged summary of bio-phylo@googlegroups.com - 1 Message in 1 Topic
Hi László, if you add a matrix row that is longer than the current nchar, more characters will be
9/13/12
László Nagy
,
Rutger Vos
2
9/12/12
adding new characters to matrix
Hi László, the list of characters is automatically updated as the matrix grows/shrinks. This is done
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adding new characters to matrix
Hi László, the list of characters is automatically updated as the matrix grows/shrinks. This is done
9/12/12
Rutger Vos
5/29/12
Fwd: [bio-phylo] Newick tree simplification (#1)
Hi all, Bio::Phylo power user has added some functionality for dealing with very large newick strings
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Fwd: [bio-phylo] Newick tree simplification (#1)
Hi all, Bio::Phylo power user has added some functionality for dealing with very large newick strings
5/29/12
László Nagy
,
Rutger Vos
2
5/8/12
Re: Abridged summary of bio-phylo@googlegroups.com - 1 Message in 1 Topic
Hi Laszlo, thanks, I hope this is useful to you. Don't hesitate to ask about how it all fits
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Re: Abridged summary of bio-phylo@googlegroups.com - 1 Message in 1 Topic
Hi Laszlo, thanks, I hope this is useful to you. Don't hesitate to ask about how it all fits
5/8/12
Rutger Vos
5/2/12
Fwd: NeXML question
Dear Laszlo, thank you very much for putting this question to me, it was actually a topic I was
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Fwd: NeXML question
Dear Laszlo, thank you very much for putting this question to me, it was actually a topic I was
5/2/12