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Efficient phylogenomic software by maximum likelihood
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uniqueseq.phy contains erroneous output when supplied with .nex file #176

Open davised opened 4 years ago

davised commented 4 years ago

Error Description

Output found in the prefix.uniqueseq.phy file is not consistent with the input alignment file. There is a replication of certain amino acids multiple times rather than the input sequence itself. This error seems linked to the nexus file as input, and does not happen when a single file is given using the -s flag.

Version

This error is correlated with iqtree2, specifically I'm using v2.1.2. The same input to iqtree 1.6.12 does not produce an erroneous uniqueseq.phy file.

Example command:

iqtree2 -p minimal_example.nex -m MFP

Contents of minimal_example.nex:

#nexus
begin sets;
        charset AAK85942.1 = AAK85942.1.aln: *;
end;

Contents of AAK85942.1.aln:

>Sinorhizobium_meliloti_BM806
MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
>Sinorhizobium_meliloti_USDA1022
MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
>Rhizobium_leguminosarum_bv._viciae_CZP1G1
MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA
>Sinorhizobium_meliloti_USDA1007
MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
>Sinorhizobium_meliloti_HM006
MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
>Sinorhizobium_meliloti_1021
MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
>Rhizobium_leguminosarum_bv._viciae_CZF1F8
MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA
>Sinorhizobium_meliloti_2119
MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
>Sinorhizobium_meliloti_DSM_23914
MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
>Rhizobium_leguminosarum_bv._viciae_SEP5D7
MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA
>Sinorhizobium_meliloti_2011
MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
>Rhizobium_leguminosarum_bv._viciae_USDA_2370
MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA
>Sinorhizobium_meliloti_USDA1005
MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
>Rhizobium_leguminosarum_bv._phaseoli_4292
MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA

Contents of minimal_example.nex.uniqueseq.phy:

5 649
Sinorhizobium_meliloti_BM806              MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCSSSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFTTEEEEEEQQQQQQQQQQQQQQQQQQQQQQQQQQEEIITFTTQGMMMYKKAAAWHTSSYYYYYYYYKKKKDDDDVVVAQHHHSSSFVSIAAAVHNAGQHTTEVVN--------HAKRDER
Sinorhizobium_meliloti_USDA1022           MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCSSSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFTTEEEEEEQQQQQQQQQQQQQQQQQQQQQQQQQQEEIITFTTQGMMMYKKAAAWHTSSYYYYYYYYKKKKDDDDVVVAQHHHSSSFVSIAAAVHNAGQHTTEVVN--------HAKRDER
Rhizobium_leguminosarum_bv._viciae_CZP1G1 MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFSSDDDDDDQQQQQQQQQQQQQQQQQQQQQQQQQQTTVVRYVVEHLLLFTTGGGWNKGGYYYYYYYYRRRREEEEIIIVNHHHTTTLTQLSSSMQHEAKYAASSAQ-------AA---N-K
Sinorhizobium_meliloti_USDA1007           MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCSSSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFTTEEEEEEQQQQQQQQQQQQQQQQQQQQQQQQQQEEIITFTTQGMMMYKKAAAWHTSSYYYYYYYYKKKKDDDDVVVAQHHHSSSFVSIAAAVHNAGQHTTEVVN--------HAKRDER
Rhizobium_leguminosarum_bv._viciae_CZF1F8 MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFSSDDDDDDQQQQQQQQQQQQQQQQQQQQQQQQQQTTVVRYVVEHLLLFTTGGGWNKGGYYYYYYYYRRRREEEEIIIVNHHHTTTLTQLSSSMQHEAKYAASSAQ-------AA---N-K

See the repeating characters?

This does not happen if I specify the .aln file to -s.

I've attached the .nex and .aln files for your reference.

minimal_example.zip

bqminh commented 3 years ago

This is not a bug, but a feature. In this option for the partition model, IQ-TREE will printed the sorted alignment, where the alignment sites are sorted by the site patterns, not the original site index. In phylogenetics, since the sites are treated independently, the analysis should be the same, no matter how the sites are sorted. That’s the reason, why we don’t bother to change the behaviour.

Cheers Minh

On 28 Oct 2020, at 8:01 am, Ed Davis notifications@github.com wrote:

Error Description

Output found in the prefix.uniqueseq.phy file is not consistent with the input alignment file. There is a replication of certain amino acids multiple times rather than the input sequence itself. This error seems linked to the nexus file as input, and does not happen when a single file is given using the -s flag.

Version

This error is correlated with iqtree2, specifically I'm using v2.1.2. The same input to iqtree 1.6.12 does not produce an erroneous uniqueseq.phy file.

Example command:

iqtree2 -p minimal_example.nex -m MFP Contents of minimal_example.nex:

nexus

begin sets; charset AAK85942.1 = AAK85942.1.aln: *; end; Contents of AAK85942.1.aln:

Sinorhizobium_meliloti_BM806 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Sinorhizobium_meliloti_USDA1022 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Rhizobium_leguminosarum_bv._viciae_CZP1G1 MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA Sinorhizobium_meliloti_USDA1007 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Sinorhizobium_meliloti_HM006 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Sinorhizobium_meliloti_1021 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Rhizobium_leguminosarum_bv._viciae_CZF1F8 MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA Sinorhizobium_meliloti_2119 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Sinorhizobium_meliloti_DSM_23914 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Rhizobium_leguminosarum_bv._viciae_SEP5D7 MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA Sinorhizobium_meliloti_2011 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Rhizobium_leguminosarum_bv._viciae_USDA_2370 MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA Sinorhizobium_meliloti_USDA1005 MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA Rhizobium_leguminosarum_bv._phaseoli_4292 MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA Contents of minimal_example.nex.uniqueseq.phy:

5 649 Sinorhizobium_meliloti_BM806 MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCSSSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFTTEEEEEEQQQQQQQQQQQQQQQQQQQQQQQQQQEEIITFTTQGMMMYKKAAAWHTSSYYYYYYYYKKKKDDDDVVVAQHHHSSSFVSIAAAVHNAGQHTTEVVN--------HAKRDER Sinorhizobium_meliloti_USDA1022 MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCSSSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFTTEEEEEEQQQQQQQQQQQQQQQQQQQQQQQQQQEEIITFTTQGMMMYKKAAAWHTSSYYYYYYYYKKKKDDDDVVVAQHHHSSSFVSIAAAVHNAGQHTTEVVN--------HAKRDER Rhizobium_leguminosarum_bv._viciae_CZP1G1 MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFSSDDDDDDQQQQQQQQQQQQQQQQQQQQQQQQQQTTVVRYVVEHLLLFTTGGGWNKGGYYYYYYYYRRRREEEEIIIVNHHHTTTLTQLSSSMQHEAKYAASSAQ-------AA---N-K Sinorhizobium_meliloti_USDA1007 MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCSSSEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFTTEEEEEEQQQQQQQQQQQQQQQQQQQQQQQQQQEEIITFTTQGMMMYKKAAAWHTSSYYYYYYYYKKKKDDDDVVVAQHHHSSSFVSIAAAVHNAGQHTTEVVN--------HAKRDER Rhizobium_leguminosarum_bv._viciae_CZF1F8 MMMMMMMMMMMMAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKKVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVVIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDDLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNNNNNNNSSSSSSSSSSSSSSSSSSSSSSSSSSSCCAAAEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEEERRRRRRRRRRRRRRRRRRRRRPPPPPPPPPPPPPPPPPPPPPFFFFFFFFFFFFFFSSDDDDDDQQQQQQQQQQQQQQQQQQQQQQQQQQTTVVRYVVEHLLLFTTGGGWNKGGYYYYYYYYRRRREEEEIIIVNHHHTTTLTQLSSSMQHEAKYAASSAQ-------AA---N-K See the repeating characters?

This does not happen if I specify the .aln file to -s.

I've attached the .nex and .aln files for your reference.

minimal_example.zip https://github.com/Cibiv/IQ-TREE/files/5448109/minimal_example.zip — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/Cibiv/IQ-TREE/issues/176, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADRTPUYKH73ZL372QW7YG2TSM4YJHANCNFSM4TBMOC6Q.

davised commented 3 years ago

Hi Minh,

Maybe I wasn't clear. Here is the output when I run iqtree2 -s AAK85942.1.aln -m MFP

$ cat AAK85942.1.aln.uniqueseq.phy
4 649
Sinorhizobium_meliloti_BM806              MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
Sinorhizobium_meliloti_USDA1022           MAKVIGIDLGTTNSCVSVMDGKDAKVIENAEGARTTPSMVAFTEDGERLVGQPAKRQAVTNPENTLFAIKRLIGRTFEDPTTQKDKGMVPYKIVKADNGDAWVEAHGTSYSPSQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGKIAGLDVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISVLEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLASEFKKEQGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTMKLSRAKFESLVEDLIQKTIAPCKAALKDAGVSAAEIDEVVLVGGMTRMPKVQETVKQLFGKEPHKGVNPDEVVAMGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQVFSTADDNQSAVTIRVSQGEREMAADNKLLGQFDLVGIPPAPRGVPQIEVTFDIDANGIVQVSAKDKGTGKEHQIRIQASGGLSDAEIEKMVKDAEANAEADKKRREGVEAKNQAESLVHSSEKSLQEHGDKVSETDRKAIEDAIAALKSAVEVSEPDAEDIKAKTNTLMEVSMKLGQAIYEAQQT--DAA--HADAAA-DAKR--S-GDDVVDADYEEVKDEDDRKRSA
Rhizobium_leguminosarum_bv._viciae_CZP1G1 MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA
Rhizobium_leguminosarum_bv._viciae_CZF1F8 MAKVIGIDLGTTNSCVAVMDGKDAKVIENAEGARTTPSMVAFSDDGERLVGQPAKRQAVTNPTNTLFAVKRLIGRRYEDPTVEKDKHLVPFTIVKGDNGDAWVEANGKGYSPAQISAMILQKMKETAESYLGEKVEKAVITVPAYFNDAQRQATKDAGRIAGLEVLRIINEPTAAALAYGLDKKEGKTIAVYDLGGGTFDISILEIGDGVFEVKSTNGDTFLGGEDFDMRLVEYLVAEFKRDNGIDLKNDKLALQRLKEAAEKAKIELSSSQQTEINLPFITADASGPKHLTLKLTRAKLESLVDDLVQRTIAPCKAALKDAGVTAAEIDEVVLVGGMSRMPKVQEVVKQLFGKEPHKGVNPDEVVALGAAIQAGVLQGDVKDVLLLDVTPLSLGIETLGGVFTRLIERNTTIPTKKSQTFSTAEDNQQAVTIRVSQGEREMAADNKLLGQFDLVGLPPSPRGMPQIEVTFDIDANGIVQVSAKDKGTGKEQQIRIQASGGLSDADIEKMVKDAEAHATEDKKRREAVEARNQAESLIHSSEKSLKDYGDKVSEADRTAISDAIAALKTASEASEPDADDIKAKTQTLMEVSMKLGQAIYEAQQA--ESG-AAGDASA-E-----G-GDNVVDADYEEIKD-DDRKKSA

This .phy file is not the same as when it's run with iqtree2 -p minimal_example.nex -m MFP as I showed above.

davised commented 3 years ago

If this is intended, why is the output different when specifying a file with -p file.nex compared to -s file.aln?

davised commented 3 years ago

I ran the emboss pepstats and the composition is the same between the alignments, of course!

You might make a note in the documentation somewhere that the partitioned alignments are sorted so that others don't get as confused as I was.

Thanks again for the help and the great software!