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bio-phylo

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Max Telford, Rutger Vos4

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

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 Vos2

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 Vos6

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 Vos6

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 Vos8

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 Vos4

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 Vos5

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 Vos7

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 Vos3

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 Vos3

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 Vos5

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

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 Vos3

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 Vos2

1/7/13

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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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 Vos3

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

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 Vos2

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

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 Vos2

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 Vos2

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

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 Vos2

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

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

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