RAxML output for r8s

249 views

Skip to first unread message

Michał T. Lorenc

unread,

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

unread,

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

unread,

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 )

Thank you in advance,

Michal

--
You received this message because you are subscribed to a topic in the Google Groups "raxml" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe.
To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/raxml/eef0c741-d920-4d05-a695-4e04d59e9639n%40googlegroups.com.

Alexandros Stamatakis

unread,

Apr 1, 2021, 5:29:53 AM4/1/21

to ra...@googlegroups.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>
> )
>
> 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>)

> 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,

> 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
> * 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

> to make ultrametric),and then you can specify one or more
> 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.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe

> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>.

> To unsubscribe from this group and all its topics, send an email to
> raxml+un...@googlegroups.com

> <mailto:raxml+un...@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?utm_medium=email&utm_source=footer>.
>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.

> To view this discussion on the web visit

> https://groups.google.com/d/msgid/raxml/CABMg7%3Dn7YEW6ANcK5YbC6pEU6%2BGrMcPS-5oCGmKsZYCJy8MtSg%40mail.gmail.com
> <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

unread,

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

How do I determine the number of sites in the alignment used to estimate the species tree?

Thank you in advance,

Michal

To unsubscribe from this topic, visit https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe.
To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/raxml/706badfb-a587-4319-6938-14413d9218a7%40gmail.com.

Alexandros Stamatakis

unread,

Apr 13, 2021, 1:51:48 PM4/13/21

to ra...@googlegroups.com

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

> >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
>
> 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

> <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

> <mailto:raxml%2Bunsu...@googlegroups.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>
> >

> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to raxml+un...@googlegroups.com

> <mailto:raxml%2Bunsu...@googlegroups.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/CABMg7%3Dn7YEW6ANcK5YbC6pEU6%2BGrMcPS-5oCGmKsZYCJy8MtSg%40mail.gmail.com
> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dn7YEW6ANcK5YbC6pEU6%2BGrMcPS-5oCGmKsZYCJy8MtSg%40mail.gmail.com>
>
> >

> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dn7YEW6ANcK5YbC6pEU6%2BGrMcPS-5oCGmKsZYCJy8MtSg%40mail.gmail.com?utm_medium=email&utm_source=footer

> <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 <http://www.exelixis-lab.org>

>
> --
> You received this message because you are subscribed to a topic in
> the Google Groups "raxml" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>.
> To unsubscribe from this group and all its topics, send an email to
> raxml+un...@googlegroups.com

> <mailto:raxml%2Bunsu...@googlegroups.com>.

> To view this discussion on the web visit

> https://groups.google.com/d/msgid/raxml/706badfb-a587-4319-6938-14413d9218a7%40gmail.com
> <https://groups.google.com/d/msgid/raxml/706badfb-a587-4319-6938-14413d9218a7%40gmail.com>.

>
> --
> You received this message because you are subscribed to the Google
> Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to raxml+un...@googlegroups.com
> <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit

Michał T. Lorenc

unread,

Apr 13, 2021, 9:11:19 PM4/13/21

to ra...@googlegroups.com

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

To unsubscribe from this topic, visit https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe.
To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/raxml/a70b8122-86ce-6e2a-1838-b3f1e4f380d7%40gmail.com.

Alexandros Stamatakis

unread,

Apr 14, 2021, 12:20:01 AM4/14/21

to ra...@googlegroups.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:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> > > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@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>
> >
> <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>>
> > >
> >

> > >
> > > --
> > > You received this message because you are subscribed to
> the Google
> > > Groups "raxml" group.
> > > To unsubscribe from this group and stop receiving emails
> from it,
> > send
> > > an email to raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>

> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>

> >
> > --
> > You received this message because you are subscribed to a
> topic in
> > the Google Groups "raxml" group.
> > To unsubscribe from this topic, visit
> > https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>
> >

> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>>.
> > To unsubscribe from this group and all its topics, send an
> email to
> > raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>

> > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>.

> > To view this discussion on the web visit
> >
> https://groups.google.com/d/msgid/raxml/706badfb-a587-4319-6938-14413d9218a7%40gmail.com
> <https://groups.google.com/d/msgid/raxml/706badfb-a587-4319-6938-14413d9218a7%40gmail.com>
> >
> <https://groups.google.com/d/msgid/raxml/706badfb-a587-4319-6938-14413d9218a7%40gmail.com <https://groups.google.com/d/msgid/raxml/706badfb-a587-4319-6938-14413d9218a7%40gmail.com>>.
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to raxml+un...@googlegroups.com

> <mailto:raxml%2Bunsu...@googlegroups.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/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com
> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com>
>
> >
> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com?utm_medium=email&utm_source=footer

> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%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 <http://www.exelixis-lab.org>
>
> --
> You received this message because you are subscribed to a topic in
> the Google Groups "raxml" group.
> To unsubscribe from this topic, visit
> https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>.
> To unsubscribe from this group and all its topics, send an email to
> raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>.
> To view this discussion on the web visit

> https://groups.google.com/d/msgid/raxml/a70b8122-86ce-6e2a-1838-b3f1e4f380d7%40gmail.com
> <https://groups.google.com/d/msgid/raxml/a70b8122-86ce-6e2a-1838-b3f1e4f380d7%40gmail.com>.

Michał T. Lorenc

unread,

Apr 14, 2021, 8:52:07 PM4/14/21

to ra...@googlegroups.com

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

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

To unsubscribe from this topic, visit https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe.
To unsubscribe from this group and all its topics, send an email to raxml+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/raxml/7f912004-9847-5430-67d5-aeebe89020d6%40gmail.com.

Alexandros Stamatakis

unread,

Apr 14, 2021, 11:16:37 PM4/14/21

to ra...@googlegroups.com

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/
> /
> /

> Thank you in advance,
>
> Michal
> //
>

> On Wed, Apr 14, 2021 at 2:20 PM Alexandros Stamatakis
> <alexandros...@gmail.com

> <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>

> > > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> > <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>

> > > > <mailto:raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>
> > > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>

> > <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>>.

> > > >
> > > > --
> > > > You received this message because you are subscribed to
> > the Google
> > > > Groups "raxml" group.
> > > > To unsubscribe from this group and stop receiving
> emails
> > from it,
> > > send
> > > > an email to raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>

> > > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> > <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>

> > <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>>.

> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>
> >
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>>>.
> > > To unsubscribe from this group and all its topics, send an
> > email to
> > > raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>

> > > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>
> > <mailto:raxml%252Buns...@googlegroups.com
> <mailto:raxml%25252Bun...@googlegroups.com>>>.

> https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com
> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com>
> >
> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com>>

> >
> > >
> >
> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com?utm_medium=email&utm_source=footer>
> >
> <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%40mail.gmail.com?utm_medium=email&utm_source=footer <https://groups.google.com/d/msgid/raxml/CABMg7%3Dk_1%3DmBCAdrN-5uAW1MNNbDcq4yoFAy3O_1iG0beAtwkA%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 <http://www.exelixis-lab.org>

> <http://www.exelixis-lab.org <http://www.exelixis-lab.org>>
> >
> > --
> > You received this message because you are subscribed to a
> topic in
> > the Google Groups "raxml" group.
> > To unsubscribe from this topic, visit
> > https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>
> >
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe
> <https://groups.google.com/d/topic/raxml/Nqy95287fWo/unsubscribe>>.
> > To unsubscribe from this group and all its topics, send an
> email to
> > raxml+un...@googlegroups.com
> <mailto:raxml%2Bunsu...@googlegroups.com>
> > <mailto:raxml%2Bunsu...@googlegroups.com
> <mailto:raxml%252Buns...@googlegroups.com>>.
> > To view this discussion on the web visit
> >

> https://groups.google.com/d/msgid/raxml/a70b8122-86ce-6e2a-1838-b3f1e4f380d7%40gmail.com
> <https://groups.google.com/d/msgid/raxml/a70b8122-86ce-6e2a-1838-b3f1e4f380d7%40gmail.com>

> >
> <https://groups.google.com/d/msgid/raxml/a70b8122-86ce-6e2a-1838-b3f1e4f380d7%40gmail.com <https://groups.google.com/d/msgid/raxml/a70b8122-86ce-6e2a-1838-b3f1e4f380d7%40gmail.com>>.
> >
> > --
> > You received this message because you are subscribed to the Google
> > Groups "raxml" group.
> > To unsubscribe from this group and stop receiving emails from it,
> send
> > an email to raxml+un...@googlegroups.com

> <mailto:raxml%2Bunsu...@googlegroups.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/CABMg7%3DkeBNt0GKH-fiZ%3DXA%3Ds%3DzbOg2eZGgDCU_534NWf9gNH-w%40mail.gmail.com
> <https://groups.google.com/d/msgid/raxml/CABMg7%3DkeBNt0GKH-fiZ%3DXA%3Ds%3DzbOg2eZGgDCU_534NWf9gNH-w%40mail.gmail.com>
>
> >
> <https://groups.google.com/d/msgid/raxml/CABMg7%3DkeBNt0GKH-fiZ%3DXA%3Ds%3DzbOg2eZGgDCU_534NWf9gNH-w%40mail.gmail.com?utm_medium=email&utm_source=footer

> <https://groups.google.com/d/msgid/raxml/CABMg7%3DkeBNt0GKH-fiZ%3DXA%3Ds%3DzbOg2eZGgDCU_534NWf9gNH-w%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
>

> https://groups.google.com/d/msgid/raxml/7f912004-9847-5430-67d5-aeebe89020d6%40gmail.com
> <https://groups.google.com/d/msgid/raxml/7f912004-9847-5430-67d5-aeebe89020d6%40gmail.com>.

> https://groups.google.com/d/msgid/raxml/CABMg7%3D%3Dxo1LTFWDfSrLEieWSOuAu4hgAeO2emnvrLTngq2jtwQ%40mail.gmail.com
> <https://groups.google.com/d/msgid/raxml/CABMg7%3D%3Dxo1LTFWDfSrLEieWSOuAu4hgAeO2emnvrLTngq2jtwQ%40mail.gmail.com?utm_medium=email&utm_source=footer>.

Reply all

Reply to author

Forward

0 new messages