Partition file
1,535 views
Skip to first unread message
Christian Cramer
Mar 26, 2014, 5:21:23 AM3/26/14
to ra...@googlegroups.com
Hi all,
I have a small issue with my partition file I did not find out how to resolve. I am sure someone knows the solution...
My partition file is this:
DNA, gene1=1-515
DNA, gene2codon1=517-1663/3
DNA, gene2codon2=518-1663/3
DNA, gene2codon3=516-1663/3
DNA, gene3codon1=1665-2682/3
DNA, gene3codon2=1666-2682/3
DNA, gene3codon3=1664-2682/3
DNA, gene4codon1=2685-3629/3
DNA, gene4codon2=2683-3629/3
DNA, gene4codon3=2684-3629/3
DNA, gene5codon1=3631-4293/3
DNA, gene5codon2=3632-4293/3
DNA, gene5codon3=3630-4293/3
The error message I am geeting is:
ERROR trying to assign model 2 to position 518 while already model 1 has been assigned to this position.
Thank you in advance!
Bests,
Christian
Alexandros Stamatakis
Mar 26, 2014, 5:25:08 AM3/26/14
to ra...@googlegroups.com
that's weird, can you send me the input files and command line you are
using?
alexis
--
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson
www.exelixis-lab.org
using?
alexis
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson
www.exelixis-lab.org
Alexandros Stamatakis
Mar 26, 2014, 5:54:41 AM3/26/14
to ra...@googlegroups.com
Dear Christian,
There are two issues here:
1. You are using an ancient RAxML version (7.0.3), the up to date
version is v8.0.17 available at
https://github.com/stamatak/standard-RAxML
it also includes windows executables (please also have a look at the new
manual: http://sco.h-its.org/exelixis/resource/download/NewManual.pdf)
2. you need to replace "/" by "\" e.g. the entries must read:
DNA, gene2codon1=517-1663\3
Alexis
On 03/26/2014 10:21 AM, Christian Cramer wrote:
There are two issues here:
1. You are using an ancient RAxML version (7.0.3), the up to date
version is v8.0.17 available at
https://github.com/stamatak/standard-RAxML
it also includes windows executables (please also have a look at the new
manual: http://sco.h-its.org/exelixis/resource/download/NewManual.pdf)
2. you need to replace "/" by "\" e.g. the entries must read:
DNA, gene2codon1=517-1663\3
Alexis
On 03/26/2014 10:21 AM, Christian Cramer wrote:
Christian Cramer
Mar 26, 2014, 12:16:09 PM3/26/14
to ra...@googlegroups.com
Hi Alexis,
thank you for your help!
Indeed, now it works.
I am only using the old RAxML version to test my dataset. The real analysis will be done on Cipres (or another platform)
Bests,
Christian
--
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+unsubscribe@googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
Sebastian Bailey
Dec 16, 2015, 1:46:23 PM12/16/15
to raxml, christian...@googlemail.com
Hello
I am having this problem too, but updating to the latest version has not worked for me.
ERROR trying to assign model 3853 to position 4931053
while already model 0 has been assigned to this position
Example of the partition file:
DNA, ENSG00000000419=1-435
DNA, ENSG00000001084=436-2349
DNA, ENSG00000001497=2350-3534
DNA, ENSG00000001561=3535-4878
DNA, ENSG00000001630=4879-6333
DNA, ENSG00000002549=6334-7890
DNA, ENSG00000002834=7891-8397
DNA, ENSG00000003096=8398-9963
...
Actually includes 3875 lines
Many thanks
I am having this problem too, but updating to the latest version has not worked for me.
ERROR trying to assign model 3853 to position 4931053
while already model 0 has been assigned to this position
Example of the partition file:
DNA, ENSG00000000419=1-435
DNA, ENSG00000001084=436-2349
DNA, ENSG00000001497=2350-3534
DNA, ENSG00000001561=3535-4878
DNA, ENSG00000001630=4879-6333
DNA, ENSG00000002549=6334-7890
DNA, ENSG00000002834=7891-8397
DNA, ENSG00000003096=8398-9963
...
Actually includes 3875 lines
Many thanks
Alexandros Stamatakis
Dec 17, 2015, 3:40:25 AM12/17/15
to ra...@googlegroups.com
Dear Sebastian,
Can you please send me all the input data and the command line you used?
Could you also please try if this works with ExaML and let me know?
I have a suspicion what the problem could be.
Thanks,
Alexis
> <mailto:raxml+un...@googlegroups.com>.
Can you please send me all the input data and the command line you used?
Could you also please try if this works with ExaML and let me know?
I have a suspicion what the problem could be.
Thanks,
Alexis
> --
> 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
> 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
> <mailto:raxml+un...@googlegroups.com>.
Seb Bailey
Jan 4, 2016, 6:46:25 PM1/4/16
to raxml
Hi Alexis
Have you had any luck with what this problem might be. I get a similar result when trying to run the parse-examl script with my partition file:
Have you had any luck with what this problem might be. I get a similar result when trying to run the parse-examl script with my partition file:
ERROR trying to assign model 3853 to position 4931053
while already model 0 has been assigned to this position
Many thanks
Fidel Botero
Jan 5, 2016, 5:24:07 AM1/5/16
to ra...@googlegroups.com
Hello Sebastian,
This kind of errors arise when some of the specified partitions are overlapping or the length of the alignment is different from that specified in the first line of your phylip file , a check of the limits of partitions/alignement length should correct it...I can give a look to your partition file, if you want...
Cheers,
Fidel
To unsubscribe from this group and stop receiving emails from it, send an email to raxml+un...@googlegroups.com.
Fidel Botero-Castro
Alexandros Stamatakis
Jan 5, 2016, 6:49:17 AM1/5/16
to ra...@googlegroups.com
Hi Seb,
> Have you had any luck with what this problem might be. I get a similar
> result when trying to run the parse-examl script with my partition file:
That's weird, are you using the latest version of ExaML?
> ERROR trying to assign model 3853 to position 4931053
> while already model 0 has been assigned to this position
How long is your alignment?
From the partition file it seems to be 1203411 bp long, so I don't know
where the 4931053 is coming from ...
Alexis
> > an email to raxml+un...@googlegroups.com <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
> Have you had any luck with what this problem might be. I get a similar
> result when trying to run the parse-examl script with my partition file:
> ERROR trying to assign model 3853 to position 4931053
> while already model 0 has been assigned to this position
From the partition file it seems to be 1203411 bp long, so I don't know
where the 4931053 is coming from ...
Alexis
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
> > For more options, visit https://groups.google.com/d/optout
> <https://groups.google.com/d/optout>.
>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>
> www.exelixis-lab.org <http://www.exelixis-lab.org>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
> Adjunct Professor, Dept. of Ecology and Evolutionary Biology,
> University
> of Arizona at Tucson
>
NWhite
Apr 23, 2017, 10:02:49 AM4/23/17
to raxml
Hi everyone,
I am getting the same error discussed above:
"ERROR trying to assign model 0 to position 1201016 while already model 0 has been assigned to this position"
I am using RAxML 8.2.9, and get the same error with multiple datasets, and in ExaML. I have used the same files to setup a partitioned run in other phylogenetic software that does not give an error, so I do not believe my partitions are overlapping.
I'd appreciate any insight you could give.
I am getting the same error discussed above:
"ERROR trying to assign model 0 to position 1201016 while already model 0 has been assigned to this position"
I am using RAxML 8.2.9, and get the same error with multiple datasets, and in ExaML. I have used the same files to setup a partitioned run in other phylogenetic software that does not give an error, so I do not believe my partitions are overlapping.
I'd appreciate any insight you could give.
Alexey Kozlov
Apr 24, 2017, 5:19:04 AM4/24/17
to ra...@googlegroups.com
There is most probably something wrong with your partition file formatting, could you please post it here along with the
RAxML/ExaML command line you were using?
> > www.exelixis-lab.org <http://www.exelixis-lab.org> <http://www.exelixis-lab.org>
RAxML/ExaML command line you were using?
Alexey Kozlov
Apr 24, 2017, 4:06:46 PM4/24/17
to ra...@googlegroups.com
well, you have multiple overlapping regions in your file, e.g.:
82049-826904
902540-90296991
470541-4712183
576505-5772016
both within and across partitions. So I wonder how it could have worked with other software...
82049-826904
902540-90296991
470541-4712183
576505-5772016
both within and across partitions. So I wonder how it could have worked with other software...
Alexandros Stamatakis
Apr 24, 2017, 4:10:14 PM4/24/17
to ra...@googlegroups.com
thanks alexey,
nathan, and some of those bounds seem to be larger than the alignment
length of the alignment you had sent me which is:
1201015
so the error message albeit a bit cryptic means that the specific
position has been allocated to a different partition before already,
alexis
nathan, and some of those bounds seem to be larger than the alignment
length of the alignment you had sent me which is:
1201015
so the error message albeit a bit cryptic means that the specific
position has been allocated to a different partition before already,
alexis
NWhite
Apr 24, 2017, 4:16:44 PM4/24/17
to raxml
Thanks-- something must have been lost in translation between partition file formats.
Message has been deleted
Alexandros Stamatakis
Sep 4, 2017, 12:04:11 AM9/4/17
to ra...@googlegroups.com
That's weird, can you send me the MSA and partition file to my personal
email such that I can check?
Alexis
On 04.09.2017 04:23, dtsc...@ucsc.edu wrote:
> Hello everyone, I am also getting the same problem.
>
>
> ERROR trying to assign model 16 to position 1
> while already model 0 has been assigned to this position
>
>
> However, my partition file appears to be fine, as does the phylip file.
> I don't see any overlaps!
>
>
> DNA, RRNS = 1-4123
> DNA, RRNL = 4124-11485
> WAG, ATP6 = 11486-11849
> WAG, ATP8 = 11850-11963
> WAG, ATP9 = 11964-12043
> WAG, COX1 = 12044-12703
> WAG, COX2 = 12704-13036
> WAG, COX3 = 13037-13377
> WAG, CYTB = 13378-14124
> WAG, NAD1 = 14125-14527
> WAG, NAD2 = 14528-15482
> WAG, NAD3 = 15483-15801
> WAG, NAD4 = 15802-16458
> WAG, ND4L = 16459-16577
> WAG, NAD5 = 16578-17435
> WAG, NAD6 = 17436-17872
>
>
> And the header of my phylip file is:
>
> 52 17872
> AF538053 ----------- et cetera
>
>
> ...and every row has 17872 columns.
>
> The commands I ran that didn't work were:
>
>
> raxmlHPC-PTHREADS -T 60 -m GTRGAMMA -p 12345 -x 12345 -f a -#
> autoMRE -o NC012056 -s all_aln.phy -q 20170903_partition.txt -n best
> raxmlHPC -m GTRGAMMA -p 12345 -x 12345 -f a -# autoMRE -o NC012056
> -s all_aln.phy -q 20170903_partition.txt -n best
>
>
> ...using version 8.2.4.
>
> Does anyone have any ideas of what might be causing the problem? I'm at
> a loss of ideas!
email such that I can check?
Alexis
On 04.09.2017 04:23, dtsc...@ucsc.edu wrote:
> Hello everyone, I am also getting the same problem.
>
>
> ERROR trying to assign model 16 to position 1
> while already model 0 has been assigned to this position
>
>
> However, my partition file appears to be fine, as does the phylip file.
> I don't see any overlaps!
>
>
> DNA, RRNS = 1-4123
> DNA, RRNL = 4124-11485
> WAG, ATP6 = 11486-11849
> WAG, ATP8 = 11850-11963
> WAG, ATP9 = 11964-12043
> WAG, COX1 = 12044-12703
> WAG, COX2 = 12704-13036
> WAG, COX3 = 13037-13377
> WAG, CYTB = 13378-14124
> WAG, NAD1 = 14125-14527
> WAG, NAD2 = 14528-15482
> WAG, NAD3 = 15483-15801
> WAG, NAD4 = 15802-16458
> WAG, ND4L = 16459-16577
> WAG, NAD5 = 16578-17435
> WAG, NAD6 = 17436-17872
>
>
> And the header of my phylip file is:
>
> 52 17872
> AF538053 ----------- et cetera
>
>
> ...and every row has 17872 columns.
>
> The commands I ran that didn't work were:
>
>
> raxmlHPC-PTHREADS -T 60 -m GTRGAMMA -p 12345 -x 12345 -f a -#
> autoMRE -o NC012056 -s all_aln.phy -q 20170903_partition.txt -n best
> raxmlHPC -m GTRGAMMA -p 12345 -x 12345 -f a -# autoMRE -o NC012056
> -s all_aln.phy -q 20170903_partition.txt -n best
>
>
> ...using version 8.2.4.
>
> Does anyone have any ideas of what might be causing the problem? I'm at
> a loss of ideas!
>
> --
> 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>.
> For more options, visit https://groups.google.com/d/optout.
--
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
www.exelixis-lab.org
> --
> 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>.
> For more options, visit https://groups.google.com/d/optout.
--
Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Péter Poczai
Jan 19, 2018, 9:22:00 AM1/19/18
to raxml
Hi,
I'm having a similar problem.
ERROR trying to assign model 163 to position 153311
ERROR trying to assign model 163 to position 153311
while already model 0 has been assigned to this position
Partitions:
The alignment in fasta is attached.
DNA, IGS = 1-250
DNA, trnH = 251-328
DNA, IGS = 329-990
DNA, psbA = 991-2052
DNA, IGS = 2053-2302
DNA, matK = 2303-5054
DNA, IGS = 5055-6200
DNA, rps16e2 = 6201-6437
DNA, rps16i1 = 6438-7383
DNA, rps16e1 = 7384-7423
DNA, IGS = 7424-9288
DNA, trnQ = 9289-9360
DNA, IGS = 9361-9798
DNA, psbK = 9799-9984
DNA, IGS = 9985-10422
DNA, psbI = 10423-10533
DNA, IGS = 10534-10681
DNA, trnS = 10682-10775
DNA, IGS = 10776-11686
DNA, trnGe2 = 11687-11709
DNA, trnGi1 = 11710-12557
DNA, trnGe1 = 12558-12697
DNA, IGS = 12698-13287
DNA, trnR = 13288-13359
DNA, IGS = 13360-13511
DNA, atpA = 13512-15035
DNA, IGS = 15036-15096
DNA, atpFe2 = 15097-15510
DNA, atpFi1 = 15511-16299
DNA, atpFe1 = 16300-16447
DNA, IGS = 16448-16881
DNA, atpH = 16882-17127
DNA, IGS = 17128-18565
DNA, atpI = 18566-19309
DNA, IGS = 19310-19591
DNA, rps2 = 19592-20302
DNA, IGS = 20303-20548
DNA, rpoC2 = 20549-24772
DNA, IGS = 24773-24947
DNA, rpoC1e2 = 24948-26561
DNA, rpoC1i1 = 26562-27406
DNA, rpoC2e1 = 27407-27859
DNA, IGS = 27860-27864
DNA, rpoB = 27865-31078
DNA, IGS = 31079-32637
DNA, trnC = 32638-32708
DNA, IGS = 32709-33755
DNA, petN = 33756-33845
DNA, IGS = 33846-35257
DNA, psbM = 35258-35365
DNA, IGS = 35366-36574
DNA, trnD = 36575-36648
DNA, IGS = 36649-36770
DNA, trnY = 36771-36854
DNA, IGS = 36855-36913
DNA, trnE = 36914-36991
DNA, IGS = 36992-38000
DNA, trnT = 38001-38072
DNA, IGS = 38073-39668
DNA, psbD = 39669-40730
DNA, psbC = 40731-42099
DNA, IGS = 42100-42395
DNA, trnS = 42396-42488
DNA, IGS = 42489-42898
DNA, psbZ = 42899-43087
DNA, IGS = 43088-43427
DNA, trnG = 43428-43498
DNA, IGS = 43499-43831
DNA, trnfM = 43832-43905
DNA, IGS = 43906-44083
DNA, rps14 = 44084-44386
DNA, IGS = 44387-44526
DNA, psaB = 44527-46731
DNA, IGS = 46732-46757
DNA, psaA = 46758-49010
DNA, IGS = 49011-50087
DNA, ycf3e3 = 50088-50240
DNA, ycf3i2 = 50241-51091
DNA, ycf3e2 = 51092-51321
DNA, ycf3i1 = 51322-52087
DNA, ycf3e1 = 52088-52211
DNA, IGS = 52212-53236
DNA, trnS = 53237-53324
DNA, IGS = 53325-53706
DNA, rps4 = 53707-54315
DNA, IGS = 54316-54880
DNA, trnT = 54881-54955
DNA, IGS = 54956-55970
DNA, trnLe2 = 55971-56005
DNA, trnLi1 = 56006-56532
DNA, trnLe1 = 56533-56582
DNA, IGS = 56583-57336
DNA, trnF = 57337-57409
DNA, IGS = 57410-58223
DNA, ndhJ = 58224-58721
DNA, IGS = 58722-58827
DNA, ndhK = 58828-59598
DNA, ndhC = 59599-59951
DNA, IGS = 59952-61439
DNA, trnVe2 = 61440-61454
DNA, trnVi1 = 61455-62065
DNA, trnVe1 = 62066-62112
DNA, IGS = 62113-62327
DNA, trnM = 62328-62400
DNA, IGS = 62401-62654
DNA, atpE = 62655-63061
DNA, atpB = 63062-64563
DNA, IGS = 64564-65460
DNA, rbcL = 65461-66894
DNA, IGS = 66895-67498
DNA, accD = 67949-69809
DNA, IGS = 69810-70852
DNA, psaI = 70853-70963
DNA, IGS = 70964-71443
DNA, ycf4 = 71444-71998
DNA, IGS = 71999-72988
DNA, cemA = 72989-73673
DNA, IGS = 73674-73969
DNA, petA = 73970-74932
DNA, IGS = 74933-76222
DNA, psbJ = 76223-76345
DNA, IGS = 76346-76486
DNA, psbL = 76487-76603
DNA, IGS = 76604-76626
DNA, psbF = 76627-76746
DNA, IGS = 76747-76758
DNA, psbE = 76759-77010
DNA, IGS = 77011-78318
DNA, petL = 78319-78414
DNA, IGS = 78415-78653
DNA, petG = 78654-78767
DNA, IGS = 78768-78918
DNA, trnW = 78919-78993
DNA, IGS = 78994-79162
DNA, trnP = 79163-79236
DNA, IGS = 79237-79843
DNA, psaJ = 79844-79989
DNA, IGS = 79990-80545
DNA, rpl33 = 80546-80761
DNA, IGS = 80762-81014
DNA, rps18 = 81015-81356
DNA, IGS = 81357-81634
DNA, rpl20 = 81635-82108
DNA, IGS = 82109-83003
DNA, rps12e1 = 83004-83117
DNA, IGS = 83118-83286
DNA, clpPe3 = 83287-83557
DNA, clpPi2 =83558-84253
DNA, clpPe2 = 84254-84545
DNA, clpPi1 = 84546-85463
DNA, clpPe1 = 85464-85534
DNA, IGS = 85535-86089
DNA, psbB = 86090-87617
DNA, IGS = 87618-87858
DNA, psbT = 87859-87963
DNA, IGS = 87964-88046
DNA, psbN = 88047-88178
DNA, IGS = 88179-88294
DNA, psbH = 88295-88516
DNA, IGS = 88517-88651
DNA, petBe2 = 88652-88657
DNA, petBi1 = 88658-89498
DNA, petBe1 = 89499-90152
DNA, IGS = 90153-903754
DNA, petDe2 = 90375-90382
DNA, petDi1 = 90383-91181
DNA, petDe1 = 91182-91656
DNA, IGS = 91657-91889
DNA, rpoA = 91890-92904
DNA, IGS = 92905-92983
DNA, rps11 = 92984-93400
DNA, IGS = 93401-93501
DNA, rpl36 = 93502-93615
DNA, IGS = 93616-94133
DNA, rps8 = 94134-94538
DNA, IGS = 94539-94830
DNA, rpl14 = 94831-95199
DNA, IGS = 95200-95369
DNA, rpl16e2 = 95370-95765
DNA, rpl16i1 = 95766-96949
DNA, rpl16e1 = 96950-96958
DNA, IGS = 96959-97149
DNA, rps3 = 97150-97806
DNA, rpl22 = 97807-98273
DNA, IGS = 98274-98364
DNA, rps19 = 98365-98649
DNA, IGS = 98650-98730
DNA, rpl2e2 = 98731-99214
DNA, rpl2i1 = 99215-99881
DNA, rpl2e1 = 99882-100272
DNA, IGS = 100273-100290
DNA, rpl23 = 100291-100573
DNA, IGS = 100574-100892
DNA, trnI = 100893-100966
DNA, IGS = 100967-101221
DNA, ycf2 = 101222-108419
DNA, IGS = 108420-108570
DNA, ycf15 = 108571-108791
DNA, IGS = 108792-109158
DNA, trnL = 109159-109239
DNA, IGS = 109240-109807
DNA, ndhBe2 = 109808-110563
DNA, ndhBi1 = 110564-111255
DNA, ndhBe1 = 111256-112032
DNA, IGS = 112033-112329
DNA, rps7 = 112330-112797
DNA, IGS = 112798-112850
DNA, rps12e2 = 112851-112876
DNA, rps12i2 = 112877-113412
DNA, rps12e1 = 113413-113644
DNA, IGS = 113645-115444
DNA, trnV = 115445-115519
DNA, IGS = 115520-115748
DNA, rrn16 = 115749-117247
DNA, IGS = 117248-117548
DNA, trnIe2 = 117549-117585
DNA, trnIi1 = 117586-118547
DNA, trnIe1 = 118548-118581
DNA, IGS = 118582-118645
DNA, trnAe2 = 118646-118683
DNA, trnAi1 = 118684-119506
DNA, trnAe1 = 119507-119541
DNA, IGS = 119542-119703
DNA, rrn23 = 119704-122534
DNA, IGS = 122535-122636
DNA, rrn45 = 122637-122739
DNA, IGS = 122740-123013
DNA, rrn5 = 123014-123134
DNA, IGS = 123135-123459
DNA, trnR = 123460-123533
DNA, IGS = 123534-124195
DNA, trnN = 124196-124267
DNA, IGS = 124268-124718
DNA, ycf1 = 124719-133791
DNA, ndhF = 133792-136279
DNA, IGS = 136280-137229
DNA, rpl32 = 137230-137402
DNA, IGS = 137403-137482
DNA, sprA = 137483-137762
DNA, IGS = 137763-138645
DNA, trnL = 138646-138725
DNA, IGS = 138726-138850
DNA, ccsA = 138851-139843
DNA, IGS = 139844-140205
DNA, ndhD = 140206-141709
DNA, IGS = 141710-141831
DNA, psaC = 141832-142077
DNA, IGS = 142078-142356
DNA, ndhE = 142357-142662
DNA, IGS = 142663-142931
DNA, ndhG = 142932-143462
DNA, IGS = 143463-143966
DNA, ndhI = 143697-144471
DNA, IGS = 144472-144573
DNA, ndhAe2 = 144574-145112
DNA, ndhAi1 = 145113-146407
DNA, ndhAe1 = 146408-146958
DNA, ndhH = 146959-148147
DNA, IGS = 148148-148281
DNA, rps15 = 148282-148545
DNA, IGS = 148546-148990
DNA, ycf1 = 148991-153310
Cheers,
Péter
Alexandros Stamatakis
Jan 19, 2018, 10:03:39 AM1/19/18
to ra...@googlegroups.com
how long is your alignment?
it seems that position 153311 does not exist in your partition file,
maybe you have more sites in the MSA than you think you have and some
sites are not assigned a model?
The most probable cause for this is a mismatch between the number of
sites you assume in the partition file and the number of sites the MSA
really has ...
Alexis
> > an email to raxml+un...@googlegroups.com <javascript:>
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
it seems that position 153311 does not exist in your partition file,
maybe you have more sites in the MSA than you think you have and some
sites are not assigned a model?
The most probable cause for this is a mismatch between the number of
sites you assume in the partition file and the number of sites the MSA
really has ...
Alexis
> > <mailto:raxml+un...@googlegroups.com <javascript:>>.
> > For more options, visit https://groups.google.com/d/optout
> <https://groups.google.com/d/optout>.
>
> --
> 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>
> --
> Alexandros (Alexis) Stamatakis
>
> Research Group Leader, Heidelberg Institute for Theoretical Studies
> Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
>
Péter Poczai
Jan 20, 2018, 6:35:08 AM1/20/18
to raxml
Hi,
I have to do a re-alignment and check the corresponding partitions.
I'm using whole plastid genome alignments and thinking what should be the ideal way to make the analysis. I want to run the phylogeny with RAxML where I partition the alignment to each genomic part as intergenis spacer, exon, intron, gene? Would that make sense? Is it possible to assign different substitution models for each partition?
The other options is that I run PartitionFinder and split according to that. Or I apply one single model GTR+G to the entire genome alignment as suggested by jmodeltest.
Cheers
Péter
I have to do a re-alignment and check the corresponding partitions.
I'm using whole plastid genome alignments and thinking what should be the ideal way to make the analysis. I want to run the phylogeny with RAxML where I partition the alignment to each genomic part as intergenis spacer, exon, intron, gene? Would that make sense? Is it possible to assign different substitution models for each partition?
The other options is that I run PartitionFinder and split according to that. Or I apply one single model GTR+G to the entire genome alignment as suggested by jmodeltest.
Cheers
Péter
Alexandros Stamatakis
Jan 22, 2018, 4:11:57 AM1/22/18
to ra...@googlegroups.com
Dear Péter,
> I have to do a re-alignment and check the corresponding partitions.
Okay.
> I'm using whole plastid genome alignments and thinking what should be the ideal way to make the analysis. I want to run the phylogeny with RAxML where I partition the alignment to each genomic part as intergenis spacer, exon, intron, gene? Would that make sense?
I think so, but there are of course also explicit methods for
determining a partitioning scheme, however what you suggest would be the
input for PartitionFinder or some similar tool.
> Is it possible to assign different substitution models for each partition?
Not in RAxML, but in RAxML-NG (better, faster, more user-friendly) you can.
> The other options is that I run PartitionFinder and split according to that. Or I apply one single model GTR+G to the entire genome alignment as suggested by jmodeltest.
The latter is probably not a good idea as there will presumably be a too
large heterogeneity of evolutionary processes along the genome.
Alexis
>
> Cheers
> Péter
> I have to do a re-alignment and check the corresponding partitions.
> I'm using whole plastid genome alignments and thinking what should be the ideal way to make the analysis. I want to run the phylogeny with RAxML where I partition the alignment to each genomic part as intergenis spacer, exon, intron, gene? Would that make sense?
determining a partitioning scheme, however what you suggest would be the
input for PartitionFinder or some similar tool.
> Is it possible to assign different substitution models for each partition?
> The other options is that I run PartitionFinder and split according to that. Or I apply one single model GTR+G to the entire genome alignment as suggested by jmodeltest.
large heterogeneity of evolutionary processes along the genome.
Alexis
>
> Cheers
> Péter
Brian Foley
Jan 22, 2018, 9:15:42 AM1/22/18
to raxml
Hi,
Although partitioning can be a help in many cases, it can also be very helpful the look carefully at the
alignment and use other analyses to judge which regions of the alignment are good and useful and
which regions are not useful at all for the task at hand. If you are attempting to get the phylogeny of
different isolates of the same species of algae taken from one lake or sea, it is a very different problem
than comparing algae to grasses and ferns and mosses and trees and other plants.
When the sequences are very similar, the noncoding regions can be needed to pick up small changes.
When the sequences are very diverse, the noncoding regions are often beyond saturation with
mutations and/or unalignable. This can also be true of the more variable regions of the coding
regions.
Almost very alignment has some signal and some noise, and it can often be useful to throw away
some of the alignment (strip out regions that are too diverse or can't be unambiguously aligned)
with the aim of reducing noise to thus increase the signal:noise ratio.
Brian Foley, PhD
HIV Databases
Péter Poczai
Jan 24, 2018, 10:45:28 AM1/24/18
to raxml
Hi Brian,
Can you recommend me a program, which could do this?
Best,
Péter
Reply all
Reply to author
Forward
0 new messages