ancestral state id

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HA

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Aug 26, 2021, 11:49:27 AM8/26/21
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Hello all!
Before I used raxml-ng  to reconstruct ancestral state , it was giving the ancestral ids like "Node1 , Node2 and ...."
this time I'm using the same code but the id for the sequences is a number between zero and one , and these numbers are not unique. could you please help me to how make unique id for generated ancestors.
thank you!

Alexey Kozlov

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Aug 26, 2021, 4:19:39 PM8/26/21
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Hello, please post your raxml-ng command line and output files, and I will try to help.

Alexey
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HA

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Aug 27, 2021, 3:57:10 AM8/27/21
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Hi, I used this command <   raxml-ng  --ancestral --msa aligned_HA1 --tree rooted_initial_tree.tree --model GTR+G --prefix ASR   >   
this code. when I used this code previously it gave me a file for constructed sequence , and sequences were like this ( the id for sequences were unique)

Node1   TATTCAGTTCAGGGAGCAAAAGCAGGGGATAATTTCTATTAACCATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAAATTCCTGGAAATGACAACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCC
Node2   TATTCAGTTCAGGGAGCAAAAGCAGGGGATAATTTCTATTAACCATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAAATTCCTGGAAATGACAACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCC

but now I am using the same code that I used several month ago, but it gives me the constructed sequences file like this ( the ids for sequences are not unique an they are numbers , it seems numbers are support value , but I'm not sure) and I want to have unique id for each ancestor.

0.843   TATTCGTCGGCCAGAGCAAAAGCAGGGGATAATTTCTATTAATCATGAAGACCATCATTGCTTTGAGCTACATTTTCTGTCTGGCTCTCGGCCAAGACCTTCCAGGAAATGACAACAACAGCACAGCAACGCTGTGCCTGGGACATCATGCGGTGCCAAACGGAACACTAGTGAAAACAATCACAGATGATCAGATTGAAGTGACTAATGCTACTGAGCTAGTTCAGAGCTCCTCAACGGGGAAAATATGCAACAATCCTCATCGAATCCTTGATGGAATAGACTGCACACTGATAGATGCTCTATTGGGGGACCC
0.178   TATTCGTCGGCCAGAGCAAAAGCAGGGGATAATTTCTATTAATCATGAAGACCATCATTGCTTTGAGCTACATTTTCTGTCTGGCTCTCGGCCAAGACCTTCCAGGAAATGACAACAACAGCACAGCAACGCTGTGCCTGGGACATCATGCGGTGCCAAACGGAACACTAGTGAAAACAATCACAGATGATCAGATTGAAGTGACTAATGCTACTGAGCTAGTTCAGAGCTCCTCAACGGGGAAAATATGCAACAATCCTCATCGAATCCTTGATGGAATAGACTGCACACTGATAGATGCTCTATTGGGGGACCC

thanks for replying,
Hossein


Alexey Kozlov

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Aug 27, 2021, 8:46:06 AM8/27/21
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Hi Hossein.

this looks weird, could you please post raxml-ng log files for both runs?

Best,
Alexey
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HA

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Aug 27, 2021, 9:16:25 AM8/27/21
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 I'm sending those two log files, one of them is for a run which produced unique ids for ancestros. The input files for both are similar ( one of them has some more sequences so I changed it's name). 
thanks for replying,
Hossein

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ASR.raxml.unique_id_log
ASR.raxml.log

Alexey Kozlov

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Aug 27, 2021, 4:30:32 PM8/27/21
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could you please also send me the input files for the second run (with wrong ids)?
> <mailto:alexei...@gmail.com> wrote:
> >
> >     Hello, please post your raxml-ng command line and output files, and I will try to help.
> >
> >     Alexey
> >
> >     On 26.08.21 17:49, HA wrote:
> >      > Hello all!
> >      > Before I used raxml-ng  to reconstruct ancestral state , it was giving the ancestral
> ids like
> >     "Node1
> >      > , Node2 and ...."
> >      > this time I'm using the same code but the id for the sequences is a number between
> zero and
> >     one ,
> >      > and these numbers are not unique. could you please help me to how make unique id for
> generated
> >      > ancestors.
> >      > thank you!
> >      >
> >      > --
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> >      >
> >
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HA

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Aug 31, 2021, 3:00:43 AM8/31/21
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Hi Alexey,
I think last time I failed to send the file , because it was too large, so I send it again here.

Many thanks,
Hossein

On Sat, 28 Aug 2021 at 12:51, HA <abbas...@gmail.com> wrote:
Hi Alexey,
sorry I thought I've sent the files. here it is.
many thanks


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aligned_HA1_small_sample
rooted_initial_tree.tree

Alexey Kozlov

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Aug 31, 2021, 5:22:38 AM8/31/21
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Hi Hossein,

unfortunately you alignment file is incomplete. Could you please archive it or maybe upload to
google drive etc.?

Best,
Alexey

On 31.08.21 09:00, HA wrote:
> Hi Alexey,
> I think last time I failed to send the file , because it was too large, so I send it again here.
>
> Many thanks,
> Hossein
>
> On Sat, 28 Aug 2021 at 12:51, HA <abbas...@gmail.com <mailto:abbas...@gmail.com>> wrote:
>
> Hi Alexey,
> sorry I thought I've sent the files. here it is.
> many thanks
>
>
> On Fri, 27 Aug 2021 at 09:57, HA <abbas...@gmail.com <mailto:abbas...@gmail.com>> wrote:
>
> Hi, I used this command <   raxml-ng  --ancestral --msa aligned_HA1 --tree
> rooted_initial_tree.tree --model GTR+G --prefix ASR   >
> this code. when I used this code previously it gave me a file for constructed sequence , and
> sequences were like this ( the id for sequences were unique)
>
> Node1
>  TATTCAGTTCAGGGAGCAAAAGCAGGGGATAATTTCTATTAACCATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAAATTCCTGGAAATGACAACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCC
> Node2
>  TATTCAGTTCAGGGAGCAAAAGCAGGGGATAATTTCTATTAACCATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAAATTCCTGGAAATGACAACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCC
>
> but now I am using the same code that I used several month ago, but it gives me the
> constructed sequences file like this ( the ids for sequences are not unique an they are
> numbers , it seems numbers are support value , but I'm not sure) and I want to have unique
> id for each ancestor.
>
> 0.843
>  TATTCGTCGGCCAGAGCAAAAGCAGGGGATAATTTCTATTAATCATGAAGACCATCATTGCTTTGAGCTACATTTTCTGTCTGGCTCTCGGCCAAGACCTTCCAGGAAATGACAACAACAGCACAGCAACGCTGTGCCTGGGACATCATGCGGTGCCAAACGGAACACTAGTGAAAACAATCACAGATGATCAGATTGAAGTGACTAATGCTACTGAGCTAGTTCAGAGCTCCTCAACGGGGAAAATATGCAACAATCCTCATCGAATCCTTGATGGAATAGACTGCACACTGATAGATGCTCTATTGGGGGACCC
> 0.178
>  TATTCGTCGGCCAGAGCAAAAGCAGGGGATAATTTCTATTAATCATGAAGACCATCATTGCTTTGAGCTACATTTTCTGTCTGGCTCTCGGCCAAGACCTTCCAGGAAATGACAACAACAGCACAGCAACGCTGTGCCTGGGACATCATGCGGTGCCAAACGGAACACTAGTGAAAACAATCACAGATGATCAGATTGAAGTGACTAATGCTACTGAGCTAGTTCAGAGCTCCTCAACGGGGAAAATATGCAACAATCCTCATCGAATCCTTGATGGAATAGACTGCACACTGATAGATGCTCTATTGGGGGACCC
>
> thanks for replying,
> Hossein
>
>
> On Thursday, August 26, 2021 at 10:19:39 PM UTC+2 alexei...@gmail.com
> <mailto:alexei...@gmail.com> wrote:
>
> Hello, please post your raxml-ng command line and output files, and I will try to help.
>
> Alexey
>
> On 26.08.21 17:49, HA wrote:
> > Hello all!
> > Before I used raxml-ng  to reconstruct ancestral state , it was giving the ancestral
> ids like "Node1
> > , Node2 and ...."
> > this time I'm using the same code but the id for the sequences is a number between
> zero and one ,
> > and these numbers are not unique. could you please help me to how make unique id for
> generated
> > ancestors.
> > thank you!
> >
> > --
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> >
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>
> >
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HA

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Aug 31, 2021, 6:18:50 AM8/31/21
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Hi Alexey, 
I made the rar file of that, thanks for that.

Regards

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aligned_HA1.rar

Alexey Kozlov

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Aug 31, 2021, 6:35:25 AM8/31/21
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now tree file has wrong number of taxa... please double-check all files before sending!

On 31.08.21 12:18, HA wrote:
> Hi Alexey,
> I made the rar file of that, thanks for that.
>
> Regards
>
> On Tue, 31 Aug 2021 at 11:22, Alexey Kozlov <alexei...@gmail.com
> <mailto:alexei...@gmail.com>> wrote:
>
> Hi Hossein,
>
> unfortunately you alignment file is incomplete. Could you please archive it or maybe upload to
> google drive etc.?
>
> Best,
> Alexey
>
> On 31.08.21 09:00, HA wrote:
> > Hi Alexey,
> > I think last time I failed to send the file , because it was too large, so I send it again here.
> >
> > Many thanks,
> > Hossein
> >
> > On Sat, 28 Aug 2021 at 12:51, HA <abbas...@gmail.com <mailto:abbas...@gmail.com>
> <mailto:abbas...@gmail.com <mailto:abbas...@gmail.com>>> wrote:
> >
> >     Hi Alexey,
> >     sorry I thought I've sent the files. here it is.
> >     many thanks
> >
> >
> >     On Fri, 27 Aug 2021 at 09:57, HA <abbas...@gmail.com <mailto:abbas...@gmail.com>
> <mailto:abbas...@gmail.com <mailto:abbas...@gmail.com>>> wrote:
> >
> >         Hi, I used this command <   raxml-ng  --ancestral --msa aligned_HA1 --tree
> >         rooted_initial_tree.tree --model GTR+G --prefix ASR   >
> >         this code. when I used this code previously it gave me a file for constructed
> sequence , and
> >         sequences were like this ( the id for sequences were unique)
> >
> >         Node1
> >
>  TATTCAGTTCAGGGAGCAAAAGCAGGGGATAATTTCTATTAACCATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAAATTCCTGGAAATGACAACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCC
> >         Node2
> >
>  TATTCAGTTCAGGGAGCAAAAGCAGGGGATAATTTCTATTAACCATGAAGACTATCATTGCTTTGAGCTACATTCTATGTCTGGTTTTCGCTCAAAAAATTCCTGGAAATGACAACAATAGCACGGCAACGCTGTGCCTTGGGCACCATGCAGTACCAAACGGAACGATAGTGAAAACAATCACAAATGACCGAATTGAAGTTACTAATGCTACTGAGTTGGTTCAGAATTCCTCAATAGGTGAAATATGCGACAGTCCTCATCAGATCCTTGATGGAGAAAACTGCACACTAATAGATGCTCTATTGGGAGACCC
> >
> >         but now I am using the same code that I used several month ago, but it gives me the
> >         constructed sequences file like this ( the ids for sequences are not unique an they are
> >         numbers , it seems numbers are support value , but I'm not sure) and I want to have
> unique
> >         id for each ancestor.
> >
> >         0.843
> >
>  TATTCGTCGGCCAGAGCAAAAGCAGGGGATAATTTCTATTAATCATGAAGACCATCATTGCTTTGAGCTACATTTTCTGTCTGGCTCTCGGCCAAGACCTTCCAGGAAATGACAACAACAGCACAGCAACGCTGTGCCTGGGACATCATGCGGTGCCAAACGGAACACTAGTGAAAACAATCACAGATGATCAGATTGAAGTGACTAATGCTACTGAGCTAGTTCAGAGCTCCTCAACGGGGAAAATATGCAACAATCCTCATCGAATCCTTGATGGAATAGACTGCACACTGATAGATGCTCTATTGGGGGACCC
> >         0.178
> >
>  TATTCGTCGGCCAGAGCAAAAGCAGGGGATAATTTCTATTAATCATGAAGACCATCATTGCTTTGAGCTACATTTTCTGTCTGGCTCTCGGCCAAGACCTTCCAGGAAATGACAACAACAGCACAGCAACGCTGTGCCTGGGACATCATGCGGTGCCAAACGGAACACTAGTGAAAACAATCACAGATGATCAGATTGAAGTGACTAATGCTACTGAGCTAGTTCAGAGCTCCTCAACGGGGAAAATATGCAACAATCCTCATCGAATCCTTGATGGAATAGACTGCACACTGATAGATGCTCTATTGGGGGACCC
> >
> >         thanks for replying,
> >         Hossein
> >
> >
> >         On Thursday, August 26, 2021 at 10:19:39 PM UTC+2 alexei...@gmail.com
> <mailto:alexei...@gmail.com>
> >         <mailto:alexei...@gmail.com <mailto:alexei...@gmail.com>> wrote:
> >
> >             Hello, please post your raxml-ng command line and output files, and I will try to
> help.
> >
> >             Alexey
> >
> >             On 26.08.21 17:49, HA wrote:
> >              > Hello all!
> >              > Before I used raxml-ng  to reconstruct ancestral state , it was giving the
> ancestral
> >             ids like "Node1
> >              > , Node2 and ...."
> >              > this time I'm using the same code but the id for the sequences is a number between
> >             zero and one ,
> >              > and these numbers are not unique. could you please help me to how make unique
> id for
> >             generated
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HA

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Aug 31, 2021, 9:34:53 AM8/31/21
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sorry for that , I repeated the steps and now I'm sending the correct file.
thank you

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aligned_HA1.rar

Alexey Kozlov

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Aug 31, 2021, 10:37:34 AM8/31/21
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thanks, now I finally see the problem: your input tree file already has inner node names (probably
support values), and so raxml-ng reuses those names instead of generating unique ids

(in some cases user might want to provide meaningful names for inner nodes, this was clearly not
your intention here, but raxml-ng is not smart enough yet to detect this)

so just remove those support values from "rooted_initial_tree.tree", and everything should work again

On 31.08.21 15:34, HA wrote:
> sorry for that , I repeated the steps and now I'm sending the correct file.
> thank you
>
> On Tue, 31 Aug 2021 at 12:35, Alexey Kozlov <alexei...@gmail.com
> <mailto:alexei...@gmail.com>> wrote:
>
> now tree file has wrong number of taxa... please double-check all files before sending!
>
> On 31.08.21 12:18, HA wrote:
> > Hi Alexey,
> > I made the rar file of that, thanks for that.
> >
> > Regards
> >
> > On Tue, 31 Aug 2021 at 11:22, Alexey Kozlov <alexei...@gmail.com
> <mailto:alexei...@gmail.com>
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HA

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Sep 1, 2021, 4:37:23 AM9/1/21
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Hi Alexey!
Thanks for your help, I made a new initial tree but without any support value, then used that tree as input for raxml-ng and it worked as you mentioned.

Regards, 
Hossein

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Alexey Kozlov

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Sep 6, 2021, 9:42:47 AM9/6/21
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perfect, thanks for the confirmation!

On 01.09.21 10:37, HA wrote:
> Hi Alexey!
> Thanks for your help, I made a new initial tree but without any support value, then used that tree
> as input for raxml-ng and it worked as you mentioned.
>
> Regards,
> Hossein
>
> On Tue, 31 Aug 2021 at 16:37, Alexey Kozlov <alexei...@gmail.com
> <mailto:alexei...@gmail.com>> wrote:
>
> thanks, now I finally see the problem: your input tree file already has inner node names (probably
> support values), and so raxml-ng reuses those names instead of generating unique ids
>
> (in some cases user might want to provide meaningful names for inner nodes, this was clearly not
> your intention here, but raxml-ng is not smart enough yet to detect this)
>
> so just remove those support values from "rooted_initial_tree.tree", and everything should work
> again
>
> On 31.08.21 15:34, HA wrote:
> > sorry for that , I repeated the steps and now I'm sending the correct file.
> > thank you
> >
> > On Tue, 31 Aug 2021 at 12:35, Alexey Kozlov <alexei...@gmail.com
> <mailto:alexei...@gmail.com>
> > <mailto:alexei...@gmail.com <mailto:alexei...@gmail.com>>> wrote:
> >
> >     now tree file has wrong number of taxa... please double-check all files before sending!
> >
> >     On 31.08.21 12:18, HA wrote:
> >      > Hi Alexey,
> >      > I made the rar file of that, thanks for that.
> >      >
> >      > Regards
> >      >
> >      > On Tue, 31 Aug 2021 at 11:22, Alexey Kozlov <alexei...@gmail.com
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