SATe User

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This group is a forum for announcing releases and discussing issues (e.g. bugs and feature requests) related to the SATé software for multiple sequence alignment and phylogenetic reconstruction. The software is distributed from http://phylo.bio.ku.edu/software/sate/sate.html

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David Condon, Mark Holder2

4/24/20

Cannot download Sate Linux version

Apologies, the link should be to: http://phylo.bio.ku.edu/software/sate/downloads2/ all the best,

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Cannot download Sate Linux version

Apologies, the link should be to: http://phylo.bio.ku.edu/software/sate/downloads2/ all the best,

4/24/20

11/19/18

Problem while executing $ python2 run_sate.py incompatibility with current version of dendropy

Dear Kibet Gilbert, You might consider using PASTA instead of SATe (see below). The code is available

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Problem while executing $ python2 run_sate.py incompatibility with current version of dendropy

Dear Kibet Gilbert, You might consider using PASTA instead of SATe (see below). The code is available

11/19/18

Madza Y Farias-Virgens, Mark Holder3

4/5/18

Install SATe locally

Hi Mark, yes, it worked. just git checkout 08e7ffb6e8640440f1ab36157b5696d481a92ff9 and then delete

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Install SATe locally

Hi Mark, yes, it worked. just git checkout 08e7ffb6e8640440f1ab36157b5696d481a92ff9 and then delete

4/5/18

Shabnam Zaman, … Mark Holder17

3/23/17

RAxML as tree estimator causes SATe to crash

Please note that I'm running PASTA on Ubuntu via VirtualBox, whereas all the SATe runs were on my

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RAxML as tree estimator causes SATe to crash

Please note that I'm running PASTA on Ubuntu via VirtualBox, whereas all the SATe runs were on my

3/23/17

Malena Serrano Noreña, Tandy Warnow2

5/4/16

CAFe to study phylogenetic relationships with whole genome sequences

Dear Malena, SATe is not designed for whole genome alignment. The issue is that whole genomes evolve

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CAFe to study phylogenetic relationships with whole genome sequences

Dear Malena, SATe is not designed for whole genome alignment. The issue is that whole genomes evolve

5/4/16

Malena Serrano Noreña

5/4/16

SATé sorry no CAFé

In my previous question I wrote CAFé instead SATé sorry.

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SATé sorry no CAFé

In my previous question I wrote CAFé instead SATé sorry.

5/4/16

bko...@uni-potsdam.de, Mark Holder2

3/23/15

Hi, I don't think that there is a way to do that right now. I may be incorrect on that because I

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Hi, I don't think that there is a way to do that right now. I may be incorrect on that because I

3/23/15

Patricia Sanchez-Baracaldo, … Tandy Warnow3

6/12/13

Fasta files & alignment issues

Are the sequences all full-length? Tandy On Wed, Jun 12, 2013 at 3:35 PM, Jamie Oaks <joaks1@gmail

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Fasta files & alignment issues

Are the sequences all full-length? Tandy On Wed, Jun 12, 2013 at 3:35 PM, Jamie Oaks <joaks1@gmail

6/12/13

yumeng wang, Jamie Oaks3

5/8/13

Can SATe output distance matrix?

Thanks a lot! 2013/5/8 Jamie Oaks <joa...@gmail.com> Hi Yumeng, Thank you for your post. The

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Can SATe output distance matrix?

Thanks a lot! 2013/5/8 Jamie Oaks <joa...@gmail.com> Hi Yumeng, Thank you for your post. The

5/8/13

Yecheng Huang, Jamie Oaks5

3/8/13

Thanks a lot for the suggestion,

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Thanks a lot for the suggestion,

3/8/13

2/15/13

New Release: SATe 2.2.7

Version 2.2.7 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

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New Release: SATe 2.2.7

Version 2.2.7 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

2/15/13

2/15/13

New Release: SATe 2.2.6

Version 2.2.6 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

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New Release: SATe 2.2.6

Version 2.2.6 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

2/15/13

Kathleen Brown, … Jamie Oaks5

2/9/13

installing SATe on a linux cluster

Thank you both for your replies. Sorry it took me a bit to get back to you - shortly after I posted

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installing SATe on a linux cluster

Thank you both for your replies. Sorry it took me a bit to get back to you - shortly after I posted

2/9/13

Nam Nguyen, Jamie Oaks2

1/29/13

SATe fails to decompose small datasets

Hi Nam, Thanks for your post. Mark and I discussed this issue and decided that the current behavior

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SATe fails to decompose small datasets

Hi Nam, Thanks for your post. Mark and I discussed this issue and decided that the current behavior

1/29/13

10/16/12

New Release: SATe 2.2.5

Version 2.2.5 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

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New Release: SATe 2.2.5

Version 2.2.5 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

10/16/12

Matt K., Jamie Oaks5

10/9/12

Running from command line

Hi Matt, Sorry for the delay, and thanks for posting the details associated with the "refused to

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Running from command line

Hi Matt, Sorry for the delay, and thanks for posting the details associated with the "refused to

10/9/12

Andrea, Jamie Oaks3

9/14/12

You helped me a lot. Thanks! 2012/9/13 Jamie Oaks <joa...@gmail.com> Hi, These values are

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You helped me a lot. Thanks! 2012/9/13 Jamie Oaks <joa...@gmail.com> Hi, These values are

9/14/12

7/18/12

New Release: SATe 2.2.4

Version 2.2.3 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

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New Release: SATe 2.2.4

Version 2.2.3 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

7/18/12

Suman Neupane, Jamie Oaks2

5/23/12

Problem with second run

Hi Suman, The SATe GUI should only let you check that box if all the sequences in your input file are

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Problem with second run

Hi Suman, The SATe GUI should only let you check that box if all the sequences in your input file are

5/23/12

5/20/12

New Release: SATe 2.2.3

Version 2.2.3 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

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New Release: SATe 2.2.3

Version 2.2.3 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

5/20/12

5/16/12

New Release: SATe 2.2.2

Version 2.2.2 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

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New Release: SATe 2.2.2

Version 2.2.2 of SATe has just been released: http://phylo.bio.ku.edu/software/sate/sate.html Updates

5/16/12

kirti prakash, Mark Holder2

5/14/12

input parsing error

Hi Kirti, Hmmm. There should not be a constraint on the names (though the first character in the line

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input parsing error

Hi Kirti, Hmmm. There should not be a constraint on the names (though the first character in the line

5/14/12

5/12/12

Bug causing the tree breaking strategy to be the centroid option

Hi all, We have just discovered that a bug has caused SATé to use 'centroid' tree

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Bug causing the tree breaking strategy to be the centroid option

Hi all, We have just discovered that a bug has caused SATé to use 'centroid' tree

5/12/12

5/7/12

New Release: SATe 2.2.1

Version 2.2.1 of SATe was released on Friday: http://phylo.bio.ku.edu/software/sate/sate.html Updates

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New Release: SATe 2.2.1

Version 2.2.1 of SATe was released on Friday: http://phylo.bio.ku.edu/software/sate/sate.html Updates

5/7/12

Jamie Oaks, Patricia Sanchez-Baracaldo4

5/1/12

New Release: SATe 2.2.0

Hi Jamie, I just worked our that Sate like to be in the applications folder. I have Mac 10.6.8 -

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New Release: SATe 2.2.0

Hi Jamie, I just worked our that Sate like to be in the applications folder. I have Mac 10.6.8 -

5/1/12

5/1/12

Bug found in SATe v2.1.0

This bug is fixed in version 2.2.0 of SATe, which is now available for download at the SATe website:

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Bug found in SATe v2.1.0

This bug is fixed in version 2.2.0 of SATe, which is now available for download at the SATe website:

5/1/12

Rebecca Buckley, … Mark Holder4

4/26/12

new user - error message

Hi Rebecca, This appears to be a case in which RAxML is running out of memory. The alignment at this

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new user - error message

Hi Rebecca, This appears to be a case in which RAxML is running out of memory. The alignment at this

4/26/12

Patricia Sanchez-Baracaldo, … Mark Holder14

4/25/12

Sate errors using more than one gene, formatting data and bootstrap using raxml

Hi, We should be able to fix both of those issues in the next couple of weeks. RAxML will deal with

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Sate errors using more than one gene, formatting data and bootstrap using raxml

Hi, We should be able to fix both of those issues in the next couple of weeks. RAxML will deal with

4/25/12

1/3/12

a request for feedback from SATe users

Dear SATé users, We are writing to all the users of the SATé software, in preparation for developing

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a request for feedback from SATe users

Dear SATé users, We are writing to all the users of the SATé software, in preparation for developing

1/3/12

Rohan Maddamsetti, Mark Holder3

12/13/11

specifying aligner options through SATe

Thanks for your quick and thorough reply, Mark. I tried adding '- codon' option to prank, but

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specifying aligner options through SATe

Thanks for your quick and thorough reply, Mark. I tried adding '- codon' option to prank, but

12/13/11

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