RAxML output for r8s
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Michał T. Lorenc
Mar 25, 2021, 8:53:16 PM3/25/21
to raxml
Hi Fabio,
I used https://github.com/migrau/phylopipe pipeline and as result I got the following RAxML outputs:
...
- partitions.csv
- concat.fasta
- tmpdirprankmsaghSvDH
- concat.phy
- partitions.csv.reduced
- concat.phy.reduced
- RAxML_bootstrap.outRaxml
- RAxML_info.outRaxml
- RAxML_bipartitionsBranchLabels.outRaxml
- RAxML_bipartitions.outRaxml
- RAxML_bestTree.outRaxml
Which out file should I use for r8s in order to get an ultrametric tree (time trees)?
Additionally, how to determine the number of sites in the alignment used to estimate the species tree (the one you want to make ultrametric), and then you can specify one or more calibration points (ideally, the age or age window of a documented fossil) to scale branch lengths into time unit?
The aim is to use ultrametric tree for CAFE.
Thank you in advance,
Michal
Alexis
Mar 29, 2021, 11:27:38 PM3/29/21
to raxml
You should use the RAxML_bestTree.outRaxml file, but it might need to be converted to Nexus format (the RAxML output is in Newick). But this one is a file with a single tree. You could also use the trees contained in RAxML_bootstrap.outRaxml to obtain a broader sampling of tree topologies and branch lengths (this is what I would recommend). Alternatively you could also use a so-called plausible tree set (see https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946) which is equally good or maybe eben better than using the BS trees.
Alexis
Michał T. Lorenc
Mar 31, 2021, 10:10:33 PM3/31/21
to ra...@googlegroups.com
Thank you. How is it possible to determine the following values:
"... You will need to know the number of sites in the alignment used to estimate the species tree (the one you want to make ultrametric),and then you can specify one or more calibration points (ideally, the age or age window of a documented fossil) to scale branch lengths into time units. We provide you with a script that prepares the control file for running r8s on the species tree..." ( source https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution )
"... You will need to know the number of sites in the alignment used to estimate the species tree (the one you want to make ultrametric),and then you can specify one or more calibration points (ideally, the age or age window of a documented fossil) to scale branch lengths into time units. We provide you with a script that prepares the control file for running r8s on the species tree..." ( source https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution )
Thank you in advance,
Michal
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Alexandros Stamatakis
Apr 1, 2021, 5:29:53 AM4/1/21
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Just have a look at your alignment file
Alexis
On 01.04.21 05:10, Michał T. Lorenc wrote:
> Thank you. How is it possible to determine the following values:
>
> "... You will need to know the number of sites in the alignment used to
> estimate the species tree (the one you want to make ultrametric),and
> then you can specify one or more calibration points (ideally, the age or
> age window of a documented fossil) to scale branch lengths into time
> units. We provide you with a script that prepares the control file for
> running r8s on the species tree..." ( source
> https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution
> <https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution>
> )
>
> Thank you in advance,
>
> Michal
>
> On Tue, 30 Mar 2021, 1:27 pm Alexis, <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> wrote:
>
> You should use the RAxML_bestTree.outRaxml file, but it might need
> to be converted to Nexus format (the RAxML output is in Newick). But
> this one is a file with a single tree. You could also use the trees
> contained in RAxML_bootstrap.outRaxml to obtain a broader sampling
> of tree topologies and branch lengths (this is what I would
> recommend). Alternatively you could also use a so-called plausible
> tree set (see
> https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946
> <https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946>)
> * concat.fasta
> * tmpdirprankmsaghSvDH
> * concat.phy
> * partitions.csv.reduced
> * concat.phy.reduced
> * RAxML_bootstrap.outRaxml
> * RAxML_info.outRaxml
> * RAxML_bipartitionsBranchLabels.outRaxml
> * RAxML_bipartitions.outRaxml
> * RAxML_bestTree.outRaxml
>
> --
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--
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
www.exelixis-lab.org
Alexis
On 01.04.21 05:10, Michał T. Lorenc wrote:
> Thank you. How is it possible to determine the following values:
>
> "... You will need to know the number of sites in the alignment used to
> estimate the species tree (the one you want to make ultrametric),and
> then you can specify one or more calibration points (ideally, the age or
> age window of a documented fossil) to scale branch lengths into time
> units. We provide you with a script that prepares the control file for
> running r8s on the species tree..." ( source
> https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution
> <https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution>
> )
>
> Thank you in advance,
>
> Michal
>
> On Tue, 30 Mar 2021, 1:27 pm Alexis, <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> wrote:
>
> You should use the RAxML_bestTree.outRaxml file, but it might need
> to be converted to Nexus format (the RAxML output is in Newick). But
> this one is a file with a single tree. You could also use the trees
> contained in RAxML_bootstrap.outRaxml to obtain a broader sampling
> of tree topologies and branch lengths (this is what I would
> recommend). Alternatively you could also use a so-called plausible
> tree set (see
> https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946
> which is equally good or maybe eben better than using the BS trees.
>
> Alexis
>
> m.t.l...@gmail.com <mailto:m.t.l...@gmail.com> schrieb am Freitag,
>
> Alexis
>
> 26. März 2021 um 02:53:16 UTC+2:
>
> Hi Fabio,
> I used https://github.com/migrau/phylopipe
> <https://github.com/migrau/phylopipe> pipeline and as result I
> got the following RAxML outputs:
> ...
>
> * partitions.csv
>
> Hi Fabio,
> I used https://github.com/migrau/phylopipe
> <https://github.com/migrau/phylopipe> pipeline and as result I
> got the following RAxML outputs:
> ...
>
> * concat.fasta
> * tmpdirprankmsaghSvDH
> * concat.phy
> * partitions.csv.reduced
> * concat.phy.reduced
> * RAxML_bootstrap.outRaxml
> * RAxML_info.outRaxml
> * RAxML_bipartitionsBranchLabels.outRaxml
> * RAxML_bipartitions.outRaxml
> * RAxML_bestTree.outRaxml
>
> Which out file should I use for r8s in order to get an
> ultrametric tree (time trees)?
>
> Additionally, how to determine the number of sites in
> thealignment used to estimate the species tree (the one you want
> Which out file should I use for r8s in order to get an
> ultrametric tree (time trees)?
>
> Additionally, how to determine the number of sites in
> to make ultrametric),and then you can specify one or more
> calibration points (ideally, the age or age window ofa
> calibration points (ideally, the age or age window ofa
> documented fossil) to scale branch lengths into time unit?
>
> The aim is to use ultrametric tree for CAFE.
>
> Thank you in advance,
>
> Michal
>
> --
> You received this message because you are subscribed to a topic in
> the Google Groups "raxml" group.
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> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>.
>
> The aim is to use ultrametric tree for CAFE.
>
> Thank you in advance,
>
> Michal
>
> --
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> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dn7YEW6ANcK5YbC6pEU6%2BGrMcPS-5oCGmKsZYCJy8MtSg%40mail.gmail.com?utm_medium=email&utm_source=footer>.
--
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
www.exelixis-lab.org
Michał T. Lorenc
Apr 13, 2021, 9:09:24 AM4/13/21
to ra...@googlegroups.com
Thank you, but I have 13911 files generated by muscled.
$ head micrurus0015734.fasta
>Natt|transcript:OIT04750
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVY--
>Nlab|nlab-chr10.g9565.t1
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
>Nqld|nqld-chr11_pilon3.g3322.t1
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
>Nsyl|NisylKD949204g0003.1
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
>Ntab|Nitab4.5_0011786g0010.1
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
>Natt|transcript:OIT04750
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVY--
>Nlab|nlab-chr10.g9565.t1
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
>Nqld|nqld-chr11_pilon3.g3322.t1
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
>Nsyl|NisylKD949204g0003.1
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
>Ntab|Nitab4.5_0011786g0010.1
MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
How do I determine the number of sites in the alignment used to estimate the species tree?
Thank you in advance,
Michal
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Alexandros Stamatakis
Apr 13, 2021, 1:51:48 PM4/13/21
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Which tool did you use to estimate the species tree?
If you used RAxML-NG you can find this data in the output files.
Alexis
On 13.04.21 16:09, Michał T. Lorenc wrote:
> Thank you, but I have 13911 files generated by muscled.
>
> /$ head micrurus0015734.fasta
> <mailto:raxml%2Bunsu...@googlegroups.com>
> > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
> > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
> <https://groups.google.com/d/msgid/raxml/706badfb-a587-4319-6938-14413d9218a7%40gmail.com>.
> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com?utm_medium=email&utm_source=footer>.
If you used RAxML-NG you can find this data in the output files.
Alexis
On 13.04.21 16:09, Michał T. Lorenc wrote:
> Thank you, but I have 13911 files generated by muscled.
>
> >Natt|transcript:OIT04750
> MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVY--
> >Nlab|nlab-chr10.g9565.t1
> MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
> >Nqld|nqld-chr11_pilon3.g3322.t1
> MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
> >Nsyl|NisylKD949204g0003.1
> MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
> >Ntab|Nitab4.5_0011786g0010.1
> MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG/
> MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVY--
> >Nlab|nlab-chr10.g9565.t1
> MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
> >Nqld|nqld-chr11_pilon3.g3322.t1
> MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
> >Nsyl|NisylKD949204g0003.1
> MADWGPVLIAVVLFVLLSPGLLFQLPGRGKVVEFGGMQTSGAAILVHTVIYFGLITILLIAVGVHVYTG
> >Ntab|Nitab4.5_0011786g0010.1
>
> How do I determine the number of sites in the alignment used to estimate
> the species tree?
>
> Thank you in advance,
>
> Michal
>
> On Thu, Apr 1, 2021 at 7:29 PM Alexandros Stamatakis
> <alexandros...@gmail.com
> How do I determine the number of sites in the alignment used to estimate
> the species tree?
>
> Thank you in advance,
>
> Michal
>
> On Thu, Apr 1, 2021 at 7:29 PM Alexandros Stamatakis
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>> wrote:
>
> Just have a look at your alignment file
>
> Alexis
>
> On 01.04.21 05:10, Michał T. Lorenc wrote:
> > Thank you. How is it possible to determine the following values:
> >
> > "... You will need to know the number of sites in the alignment
> used to
> > estimate the species tree (the one you want to make ultrametric),and
> > then you can specify one or more calibration points (ideally, the
> age or
> > age window of a documented fossil) to scale branch lengths into time
> > units. We provide you with a script that prepares the control
> file for
> > running r8s on the species tree..." ( source
> >
> https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution
> <https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution>
>
> >
> <https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution
> <https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution>>
>
> > )
> >
> > Thank you in advance,
> >
> > Michal
> >
> > On Tue, 30 Mar 2021, 1:27 pm Alexis,
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> > <mailto:alexandros...@gmail.com
>
> Just have a look at your alignment file
>
> Alexis
>
> On 01.04.21 05:10, Michał T. Lorenc wrote:
> > Thank you. How is it possible to determine the following values:
> >
> > "... You will need to know the number of sites in the alignment
> used to
> > estimate the species tree (the one you want to make ultrametric),and
> > then you can specify one or more calibration points (ideally, the
> age or
> > age window of a documented fossil) to scale branch lengths into time
> > units. We provide you with a script that prepares the control
> file for
> > running r8s on the species tree..." ( source
> >
> https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution
> <https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution>
>
> >
> <https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution
> <https://studyres.com/doc/22320765/cafe--computational-analysis-of-gene-family-evolution>>
>
> > )
> >
> > Thank you in advance,
> >
> > Michal
> >
> > On Tue, 30 Mar 2021, 1:27 pm Alexis,
> <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
> <mailto:alexandros...@gmail.com>>> wrote:
> >
> > You should use the RAxML_bestTree.outRaxml file, but it might
> need
> > to be converted to Nexus format (the RAxML output is in
> Newick). But
> > this one is a file with a single tree. You could also use the
> trees
> > contained in RAxML_bootstrap.outRaxml to obtain a broader
> sampling
> > of tree topologies and branch lengths (this is what I would
> > recommend). Alternatively you could also use a so-called
> plausible
> > tree set (see
> >
> https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946
> <https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946>
> >
> <https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946 <https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946>>)
> > which is equally good or maybe eben better than using the BS
> trees.
> >
> > Alexis
> >
> > m.t.l...@gmail.com <mailto:m.t.l...@gmail.com>
> <mailto:m.t.l...@gmail.com <mailto:m.t.l...@gmail.com>> schrieb am
> >
> > You should use the RAxML_bestTree.outRaxml file, but it might
> need
> > to be converted to Nexus format (the RAxML output is in
> Newick). But
> > this one is a file with a single tree. You could also use the
> trees
> > contained in RAxML_bootstrap.outRaxml to obtain a broader
> sampling
> > of tree topologies and branch lengths (this is what I would
> > recommend). Alternatively you could also use a so-called
> plausible
> > tree set (see
> >
> https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946
> <https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946>
> >
> <https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946 <https://academic.oup.com/mbe/advance-article/doi/10.1093/molbev/msaa314/6030946>>)
> > which is equally good or maybe eben better than using the BS
> trees.
> >
> > Alexis
> >
> > m.t.l...@gmail.com <mailto:m.t.l...@gmail.com>
> > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>>.
> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/raxml/eef0c741-d920-4d05-a695-4e04d59e9639n%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/eef0c741-d920-4d05-a695-4e04d59e9639n%40googlegroups.com>
> >
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> >
> https://groups.google.com/d/msgid/raxml/eef0c741-d920-4d05-a695-4e04d59e9639n%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/eef0c741-d920-4d05-a695-4e04d59e9639n%40googlegroups.com>
> >
> >
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Michał T. Lorenc
Apr 13, 2021, 9:11:19 PM4/13/21
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Hi Alexis,
I used conda (conda create -n phylopipe orthomcl snakemake biopython pyfasta diamond muscle prank raxml bioawk) to install raxml. However, the actual command was raxmlHPC.
Do you know which file contains the number of sites in the alignment used to estimate the species tree?
Thank you in advance,
Michal
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Alexandros Stamatakis
Apr 14, 2021, 12:20:01 AM4/14/21
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This should be contained in the RAxML_info file.
Alexis
On 14.04.21 04:11, Michał T. Lorenc wrote:
> Hi Alexis,
> I used conda /(conda create -n phylopipe orthomcl snakemake biopython
> pyfasta diamond muscle prank *raxml* bioawk) to install raxml. However,
> the actual command was raxmlHPC./
> /
> /
> > <mailto:raxml%2Bunsu...@googlegroups.com
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Alexis
On 14.04.21 04:11, Michał T. Lorenc wrote:
> Hi Alexis,
> pyfasta diamond muscle prank *raxml* bioawk) to install raxml. However,
> the actual command was raxmlHPC./
> /
> /
> Do you know which file contains the number of sites in the alignment
> used to estimate the species tree?
>
> Thank you in advance,
> Michal
> //
> used to estimate the species tree?
>
> Thank you in advance,
> Michal
> <mailto:raxml%252Buns...@googlegroups.com>>
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>
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>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
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>
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Michał T. Lorenc
Apr 14, 2021, 8:52:07 PM4/14/21
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Would 2044609 be the number of sites in the alignment used?
$ cat RAxML_info
Alignment has 148 completely undetermined sites that will be automatically removed from the input data
...
Alignment has 2044609 distinct alignment patterns
GAMMA Model parameters will be estimated up to an accuracy of 0.1000000000 Log Likelihood units
Proportion of gaps and completely undetermined characters in this alignment: 11.78%
RAxML rapid bootstrapping and subsequent ML search
Using 13911 distinct models/data partitions with joint branch length optimization
Executing 100 rapid bootstrap inferences and thereafter a thorough ML search
All free model parameters will be estimated by RAxML
GAMMA model of rate heterogeneity, ML estimate of alpha-parameter
Thank you in advance,
Michal
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Alexandros Stamatakis
Apr 14, 2021, 11:16:37 PM4/14/21
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Well not exactly, it's the number of unique site patterns, so sites that
are identical are counted only once. e.g., if you have an MSA with 10
sites, where 3 sites are identical the number of site patterns will be 8
Alexis
On 15.04.21 03:51, Michał T. Lorenc wrote:
>
> Would *2044609* be thenumber of sites in the alignment used?
>
> /$ cat RAxML_info/
> /Alignment has 148 completely undetermined sites that will be
> automatically removed from the input data/
> /.../
> /Alignment has *2044609* distinct alignment patterns/
> /
> /
> /Proportion of gaps and completely undetermined characters in this
> alignment: 11.78%/
> /
> /
> /RAxML rapid bootstrapping and subsequent ML search/
> /
> /
> /Using 13911 distinct models/data partitions with joint branch length
> optimization/
> /
> /
> /Executing 100 rapid bootstrap inferences and thereafter a thorough ML
> search /
> /
> /
> /All free model parameters will be estimated by RAxML/
> /GAMMA model of rate heterogeneity, ML estimate of alpha-parameter/
> /
> /
> /GAMMA Model parameters will be estimated up to an accuracy of
> 0.1000000000 Log Likelihood units/
> /
> /
> > > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> > <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>
> <mailto:raxml%25252Bun...@googlegroups.com>>>>.
> <mailto:raxml%252Buns...@googlegroups.com>
> > <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>
> <mailto:raxml%25252Bun...@googlegroups.com>>>>.
> <mailto:raxml%252Buns...@googlegroups.com>
> > <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>.
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> >
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>
> >
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are identical are counted only once. e.g., if you have an MSA with 10
sites, where 3 sites are identical the number of site patterns will be 8
Alexis
On 15.04.21 03:51, Michał T. Lorenc wrote:
>
> Would *2044609* be thenumber of sites in the alignment used?
>
> /$ cat RAxML_info/
> /Alignment has 148 completely undetermined sites that will be
> automatically removed from the input data/
> /.../
> /Alignment has *2044609* distinct alignment patterns/
> /
> /
> /Proportion of gaps and completely undetermined characters in this
> alignment: 11.78%/
> /
> /
> /RAxML rapid bootstrapping and subsequent ML search/
> /
> /
> /Using 13911 distinct models/data partitions with joint branch length
> optimization/
> /
> /
> /Executing 100 rapid bootstrap inferences and thereafter a thorough ML
> search /
> /
> /
> /All free model parameters will be estimated by RAxML/
> /GAMMA model of rate heterogeneity, ML estimate of alpha-parameter/
> /
> /
> /GAMMA Model parameters will be estimated up to an accuracy of
> 0.1000000000 Log Likelihood units/
> /
> /
> Thank you in advance,
>
> Michal
> //
>
>
> Michal
> //
>
> <mailto:alexandros...@gmail.com>> wrote:
>
> This should be contained in the RAxML_info file.
>
> Alexis
>
> On 14.04.21 04:11, Michał T. Lorenc wrote:
> > Hi Alexis,
> > I used conda /(conda create -n phylopipe orthomcl snakemake
> biopython
> > pyfasta diamond muscle prank *raxml* bioawk) to install raxml.
> However,
> > the actual command was raxmlHPC./
> > /
> > /
> > Do you know which file contains the number of sites in the alignment
> > used to estimate the species tree?
> >
> > Thank you in advance,
> > Michal
> > //
> >
> > On Wed, Apr 14, 2021 at 3:51 AM Alexandros Stamatakis
> > <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
>
> This should be contained in the RAxML_info file.
>
> Alexis
>
> On 14.04.21 04:11, Michał T. Lorenc wrote:
> > Hi Alexis,
> > I used conda /(conda create -n phylopipe orthomcl snakemake
> biopython
> > pyfasta diamond muscle prank *raxml* bioawk) to install raxml.
> However,
> > the actual command was raxmlHPC./
> > /
> > /
> > Do you know which file contains the number of sites in the alignment
> > used to estimate the species tree?
> >
> > Thank you in advance,
> > Michal
> > //
> >
> > On Wed, Apr 14, 2021 at 3:51 AM Alexandros Stamatakis
> > <alexandros...@gmail.com
> <mailto:alexandros...@gmail.com>
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> >
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> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
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>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
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