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Cibiv / IQ-TREE

Efficient phylogenomic software by maximum likelihood
http://www.iqtree.org
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ERROR: Redundant double-bracket... #228

Open mickey-spongebob opened 2 years ago

mickey-spongebob commented 2 years ago

Hi IQ-TREE team,

Thank you for the great software! I'm having some trouble with the error below, when I try to run IQTREE (multicore version 2.1.4-beta COVID edition) with the -g option to constrain the tree topology.

"ERROR: Redundant double-bracket <80><98>((<80>))<80><99> with closing bracket ending at (line 1 column 417)"

The tree file I'm using as the input is here:

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))))))))root;

When I upload this file on iTOL, it plots it fine, and it seems like it works. I've tried to follow this same error posted on the Google Groups, but couldn't find a solution that works for me.

The full command is: 'iqtree -s cleaned.aln -B 1000 -alrt 1000 -T 100 -g limited_constrained_tree.txt'

I'm quite new to tree reading and understanding, and so I apologise if the issue is really straightforward, but would love some advice.

Best, kevin

heikotree commented 2 years ago

Dear Kevin,

Thank you for your interest in IQ-Tree.

This error is on then side of your treefile, not in then programm.

The mistaken double-bracket ist here:

...((Schistosoma_mansoni,Echinococcus_multilocularis))...

Trees with such backets can be visualised in tree browsers like FigTree of iTol, producing non-branching nodes like: >—----—---*< (where the stars are inner nodes of the tree, dashes are branches/edges and the larger-than and smaller-than signs denote two branches coming in or going out respectively). However, such non-branching nodes as the middle one are meaningless here and should better not exist.

You have three more of those double-brackets in your tree (IQ-Tree report always the first occurrence):

...(( (Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis) ))...

...(( ((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis) ))...

...(( ((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))) ))...

I have inserted a space after and before the double-brackets, respectively, to highlight them.

So please remove one pair of brackets around Schistosoma_mansoni and Echinococcus_multilocularis and also the other three cases, then everything should work fine.

BTW, you can typically recognize such cases in a tree viewer such as FigTree (I have not checked iTol), because the branches are twice as long compared to the others, because all braches are set of a uniform length since no lengths are stated. (This would not be as obvious if you have branch lengths in your tree.)

Please note - in the case given branch lengths, one need to sum up the branch lengths of the two (or more) brackets, as for instance:

...((Hsap:0.1,Chimp:0.08):0.3):0.4...

merges to

...(Hsap:0.1,Chimp:0.08):0.7...

because of 0.3+0.4=0.7

I hope this is useful to you.

Best wishes, Heiko

On 12.04.2022, at 06:14, mickey-spongebob @.***> wrote:

Hi IQ-TREE team,

Thank you for the great software! I'm having some trouble with the error below, when I try to run IQTREE (multicore version 2.1.4-beta COVID edition) with the -g option to constrain the tree topology.

"ERROR: Redundant double-bracket <80><98>((<80>))<80><99> with closing bracket ending at (line 1 column 417)"

The tree file I'm using as the input is here:

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))))))))root;

When I upload this file on iTOL, it plots it fine, and it seems like it works. I've tried to follow this same error posted on the Google Groups, but couldn't find a solution that works for me.

The full command is: 'iqtree -s cleaned.aln -B 1000 -alrt 1000 -T 100 -g limited_constrained_tree.txt'

I'm quite new to tree reading and understanding, and so I apologise if the issue is really straightforward, but would love some advice.

Best, kevin

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

Heiko Schmidt Vienna, Austria

mickey-spongebob commented 2 years ago

Dear Heiko,

Thank you for taking the time to look at my issue. Unfortunately, after deleting all the brackets you recommended, the tree is no longer displaying the animal relationships as intended, and running IQTREE still returns the same Redundant double-bracket error.

Here is the tree that I fed as input. Just in case I made a major error when deleting.

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),((Schistosoma_mansoni,Echinococcus_multilocularis),((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis),((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))));

As this is a tree problem and not an IQTREE program issue, I understand it may be too cumbersome to deal with. Thank you nevertheless for your help :-)

Best, kevin

On 12. Apr 2022, at 12:53, Heiko Schmidt @.***> wrote:

Dear Kevin,

Thank you for your interest in IQ-Tree.

This error is on then side of your treefile, not in then programm.

The mistaken double-bracket ist here:

...((Schistosoma_mansoni,Echinococcus_multilocularis))...

Trees with such backets can be visualised in tree browsers like FigTree of iTol, producing non-branching nodes like: >—----—---*< (where the stars are inner nodes of the tree, dashes are branches/edges and the larger-than and smaller-than signs denote two branches coming in or going out respectively). However, such non-branching nodes as the middle one are meaningless here and should better not exist.

You have three more of those double-brackets in your tree (IQ-Tree report always the first occurrence):

...(( (Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis) ))...

...(( ((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis) ))...

...(( ((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))) ))...

I have inserted a space after and before the double-brackets, respectively, to highlight them.

So please remove one pair of brackets around Schistosoma_mansoni and Echinococcus_multilocularis and also the other three cases, then everything should work fine.

BTW, you can typically recognize such cases in a tree viewer such as FigTree (I have not checked iTol), because the branches are twice as long compared to the others, because all braches are set of a uniform length since no lengths are stated. (This would not be as obvious if you have branch lengths in your tree.)

Please note - in the case given branch lengths, one need to sum up the branch lengths of the two (or more) brackets, as for instance:

...((Hsap:0.1,Chimp:0.08):0.3):0.4...

merges to

...(Hsap:0.1,Chimp:0.08):0.7...

because of 0.3+0.4=0.7

I hope this is useful to you.

Best wishes, Heiko

On 12.04.2022, at 06:14, mickey-spongebob @.***> wrote:

Hi IQ-TREE team,

Thank you for the great software! I'm having some trouble with the error below, when I try to run IQTREE (multicore version 2.1.4-beta COVID edition) with the -g option to constrain the tree topology.

"ERROR: Redundant double-bracket <80><98>((<80>))<80><99> with closing bracket ending at (line 1 column 417)"

The tree file I'm using as the input is here:

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))))))))root;

When I upload this file on iTOL, it plots it fine, and it seems like it works. I've tried to follow this same error posted on the Google Groups, but couldn't find a solution that works for me.

The full command is: 'iqtree -s cleaned.aln -B 1000 -alrt 1000 -T 100 -g limited_constrained_tree.txt'

I'm quite new to tree reading and understanding, and so I apologise if the issue is really straightforward, but would love some advice.

Best, kevin

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

Heiko Schmidt Vienna, Austria

— Reply to this email directly, view it on GitHub https://github.com/Cibiv/IQ-TREE/issues/228#issuecomment-1096567429, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMEBXCTOOHUHVLTZHDPOTI3VEVIZBANCNFSM5TFHEHVQ. You are receiving this because you authored the thread.

heikotree commented 2 years ago

Dear Kevin,

Sorry for the late answer, but I was away from my email over Easter.

The problem with your tree is that you did delete both pairs of brackets. You need to just delete one opening and the related closing bracket (for each of the 4 instances).

If you delete both opening and closing brackets then the imposed grouping is gone and you get a multifurcation as is the case in the tree you have posted below.

In the following tree I have only deleted one bracket pair each:

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,(((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),((Schistosoma_mansoni,Echinococcus_multilocularis),(((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis)),(((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))))));

This should work fine.

Best regards, Heiko

On 13.04.2022, at 06:51, mickey-spongebob @.***> wrote:

Dear Heiko,

Thank you for taking the time to look at my issue. Unfortunately, after deleting all the brackets you recommended, the tree is no longer displaying the animal relationships as intended, and running IQTREE still returns the same Redundant double-bracket error.

Here is the tree that I fed as input. Just in case I made a major error when deleting.

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),((Schistosoma_mansoni,Echinococcus_multilocularis),((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis),((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))));

As this is a tree problem and not an IQTREE program issue, I understand it may be too cumbersome to deal with. Thank you nevertheless for your help :-)

Best, kevin

On 12. Apr 2022, at 12:53, Heiko Schmidt @.***> wrote:

Dear Kevin,

Thank you for your interest in IQ-Tree.

This error is on then side of your treefile, not in then programm.

The mistaken double-bracket ist here:

...((Schistosoma_mansoni,Echinococcus_multilocularis))...

Trees with such backets can be visualised in tree browsers like FigTree of iTol, producing non-branching nodes like: >—----—---*< (where the stars are inner nodes of the tree, dashes are branches/edges and the larger-than and smaller-than signs denote two branches coming in or going out respectively). However, such non-branching nodes as the middle one are meaningless here and should better not exist.

You have three more of those double-brackets in your tree (IQ-Tree report always the first occurrence):

...(( (Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis) ))...

...(( ((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis) ))...

...(( ((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))) ))...

I have inserted a space after and before the double-brackets, respectively, to highlight them.

So please remove one pair of brackets around Schistosoma_mansoni and Echinococcus_multilocularis and also the other three cases, then everything should work fine.

BTW, you can typically recognize such cases in a tree viewer such as FigTree (I have not checked iTol), because the branches are twice as long compared to the others, because all braches are set of a uniform length since no lengths are stated. (This would not be as obvious if you have branch lengths in your tree.)

Please note - in the case given branch lengths, one need to sum up the branch lengths of the two (or more) brackets, as for instance:

...((Hsap:0.1,Chimp:0.08):0.3):0.4...

merges to

...(Hsap:0.1,Chimp:0.08):0.7...

because of 0.3+0.4=0.7

I hope this is useful to you.

Best wishes, Heiko

On 12.04.2022, at 06:14, mickey-spongebob @.***> wrote:

Hi IQ-TREE team,

Thank you for the great software! I'm having some trouble with the error below, when I try to run IQTREE (multicore version 2.1.4-beta COVID edition) with the -g option to constrain the tree topology.

"ERROR: Redundant double-bracket <80><98>((<80>))<80><99> with closing bracket ending at (line 1 column 417)"

The tree file I'm using as the input is here:

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))))))))root;

When I upload this file on iTOL, it plots it fine, and it seems like it works. I've tried to follow this same error posted on the Google Groups, but couldn't find a solution that works for me.

The full command is: 'iqtree -s cleaned.aln -B 1000 -alrt 1000 -T 100 -g limited_constrained_tree.txt'

I'm quite new to tree reading and understanding, and so I apologise if the issue is really straightforward, but would love some advice.

Best, kevin

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.

Heiko Schmidt Vienna, Austria

— Reply to this email directly, view it on GitHub https://github.com/Cibiv/IQ-TREE/issues/228#issuecomment-1096567429, or unsubscribe https://github.com/notifications/unsubscribe-auth/AMEBXCTOOHUHVLTZHDPOTI3VEVIZBANCNFSM5TFHEHVQ. You are receiving this because you authored the thread.

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Heiko Schmidt Center for Integrative Bioinformatics Vienna (CIBIV) University of Vienna / Max Perutz Labs Campus Vienna Biocenter 5 (VBC5) A-1030 Vienna, Austria

Email: heiko.schmidt(AT)univie.ac.at Tel. : ++43 +1 / 4277 - 74321 http://www.cibiv.at/

mickey-spongebob commented 2 years ago

Hi Heiko,

Please don’t apologise. And thank you once more for replying and spending time on this with me. I’ve re-ran using this same tree and it still doesn’t work. I’ve decided to try other programs to see if it works and then I’ll get back to you about this issue. This way, you don’t have to spend time on the issue. If you agree, I could close the issue and if I find a solution, i’lll reply in the thread. What do you think?

Best regards and once more, thank you very much, kevin

On 22. Apr 2022, at 11:39, Heiko Schmidt @.***> wrote:

Dear Kevin,

Sorry for the late answer, but I was away from my email over Easter.

The problem with your tree is that you did delete both pairs of brackets. You need to just delete one opening and the related closing bracket (for each of the 4 instances).

If you delete both opening and closing brackets then the imposed grouping is gone and you get a multifurcation as is the case in the tree you have posted below.

In the following tree I have only deleted one bracket pair each:

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,(((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),((Schistosoma_mansoni,Echinococcus_multilocularis),(((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis)),(((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))))));

This should work fine.

Best regards, Heiko

On 13.04.2022, at 06:51, mickey-spongebob @.***> wrote:

Dear Heiko,

Thank you for taking the time to look at my issue. Unfortunately, after deleting all the brackets you recommended, the tree is no longer displaying the animal relationships as intended, and running IQTREE still returns the same Redundant double-bracket error.

Here is the tree that I fed as input. Just in case I made a major error when deleting.

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),((Schistosoma_mansoni,Echinococcus_multilocularis),((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis),((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))));

As this is a tree problem and not an IQTREE program issue, I understand it may be too cumbersome to deal with. Thank you nevertheless for your help :-)

Best, kevin

On 12. Apr 2022, at 12:53, Heiko Schmidt @.***> wrote:

Dear Kevin,

Thank you for your interest in IQ-Tree.

This error is on then side of your treefile, not in then programm.

The mistaken double-bracket ist here:

...((Schistosoma_mansoni,Echinococcus_multilocularis))...

Trees with such backets can be visualised in tree browsers like FigTree of iTol, producing non-branching nodes like: >—----—---*< (where the stars are inner nodes of the tree, dashes are branches/edges and the larger-than and smaller-than signs denote two branches coming in or going out respectively). However, such non-branching nodes as the middle one are meaningless here and should better not exist.

You have three more of those double-brackets in your tree (IQ-Tree report always the first occurrence):

...(( (Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis) ))...

...(( ((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis) ))...

...(( ((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))) ))...

I have inserted a space after and before the double-brackets, respectively, to highlight them.

So please remove one pair of brackets around Schistosoma_mansoni and Echinococcus_multilocularis and also the other three cases, then everything should work fine.

BTW, you can typically recognize such cases in a tree viewer such as FigTree (I have not checked iTol), because the branches are twice as long compared to the others, because all braches are set of a uniform length since no lengths are stated. (This would not be as obvious if you have branch lengths in your tree.)

Please note - in the case given branch lengths, one need to sum up the branch lengths of the two (or more) brackets, as for instance:

...((Hsap:0.1,Chimp:0.08):0.3):0.4...

merges to

...(Hsap:0.1,Chimp:0.08):0.7...

because of 0.3+0.4=0.7

I hope this is useful to you.

Best wishes, Heiko

On 12.04.2022, at 06:14, mickey-spongebob @.***> wrote:

Hi IQ-TREE team,

Thank you for the great software! I'm having some trouble with the error below, when I try to run IQTREE (multicore version 2.1.4-beta COVID edition) with the -g option to constrain the tree topology.

"ERROR: Redundant double-bracket <80><98>((<80>))<80><99> with closing bracket ending at (line 1 column 417)"

The tree file I'm using as the input is here:

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))))))))root;

When I upload this file on iTOL, it plots it fine, and it seems like it works. I've tried to follow this same error posted on the Google Groups, but couldn't find a solution that works for me.

The full command is: 'iqtree -s cleaned.aln -B 1000 -alrt 1000 -T 100 -g limited_constrained_tree.txt'

I'm quite new to tree reading and understanding, and so I apologise if the issue is really straightforward, but would love some advice.

Best, kevin

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Heiko Schmidt Vienna, Austria

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heikotree commented 2 years ago

Dear Kevin,

It would be nice to understand what problem you actually have.

When you say “it still doesn’t work” - what exactly does not work? What exactly did you run using which files? And what error message did you get?

What is the actual tree you get? And what is wrong with it if you get one?

Do I understand it correctly, that you input this tree as constraint tree? Do you have additional sequences in your alignment or just the 32 that are present in the tree?

If you do not want to share this information, you may consider sending me that information directly to @.***

Best regards, Heiko

On 25.04.2022, at 08:31, mickey-spongebob @.***> wrote:

Hi Heiko,

Please don’t apologise. And thank you once more for replying and spending time on this with me. I’ve re-ran using this same tree and it still doesn’t work. I’ve decided to try other programs to see if it works and then I’ll get back to you about this issue. This way, you don’t have to spend time on the issue. If you agree, I could close the issue and if I find a solution, i’lll reply in the thread. What do you think?

Best regards and once more, thank you very much, kevin

On 22. Apr 2022, at 11:39, Heiko Schmidt @.***> wrote:

Dear Kevin,

Sorry for the late answer, but I was away from my email over Easter.

The problem with your tree is that you did delete both pairs of brackets. You need to just delete one opening and the related closing bracket (for each of the 4 instances).

If you delete both opening and closing brackets then the imposed grouping is gone and you get a multifurcation as is the case in the tree you have posted below.

In the following tree I have only deleted one bracket pair each:

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,(((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),((Schistosoma_mansoni,Echinococcus_multilocularis),(((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis)),(((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))))));

This should work fine.

Best regards, Heiko

On 13.04.2022, at 06:51, mickey-spongebob @.***> wrote:

Dear Heiko,

Thank you for taking the time to look at my issue. Unfortunately, after deleting all the brackets you recommended, the tree is no longer displaying the animal relationships as intended, and running IQTREE still returns the same Redundant double-bracket error.

Here is the tree that I fed as input. Just in case I made a major error when deleting.

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),((Schistosoma_mansoni,Echinococcus_multilocularis),((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis),((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))));

As this is a tree problem and not an IQTREE program issue, I understand it may be too cumbersome to deal with. Thank you nevertheless for your help :-)

Best, kevin

On 12. Apr 2022, at 12:53, Heiko Schmidt @.***> wrote:

Dear Kevin,

Thank you for your interest in IQ-Tree.

This error is on then side of your treefile, not in then programm.

The mistaken double-bracket ist here:

...((Schistosoma_mansoni,Echinococcus_multilocularis))...

Trees with such backets can be visualised in tree browsers like FigTree of iTol, producing non-branching nodes like: >—----—---*< (where the stars are inner nodes of the tree, dashes are branches/edges and the larger-than and smaller-than signs denote two branches coming in or going out respectively). However, such non-branching nodes as the middle one are meaningless here and should better not exist.

You have three more of those double-brackets in your tree (IQ-Tree report always the first occurrence):

...(( (Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis) ))...

...(( ((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis) ))...

...(( ((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))) ))...

I have inserted a space after and before the double-brackets, respectively, to highlight them.

So please remove one pair of brackets around Schistosoma_mansoni and Echinococcus_multilocularis and also the other three cases, then everything should work fine.

BTW, you can typically recognize such cases in a tree viewer such as FigTree (I have not checked iTol), because the branches are twice as long compared to the others, because all braches are set of a uniform length since no lengths are stated. (This would not be as obvious if you have branch lengths in your tree.)

Please note - in the case given branch lengths, one need to sum up the branch lengths of the two (or more) brackets, as for instance:

...((Hsap:0.1,Chimp:0.08):0.3):0.4...

merges to

...(Hsap:0.1,Chimp:0.08):0.7...

because of 0.3+0.4=0.7

I hope this is useful to you.

Best wishes, Heiko

On 12.04.2022, at 06:14, mickey-spongebob @.***> wrote:

Hi IQ-TREE team,

Thank you for the great software! I'm having some trouble with the error below, when I try to run IQTREE (multicore version 2.1.4-beta COVID edition) with the -g option to constrain the tree topology.

"ERROR: Redundant double-bracket <80><98>((<80>))<80><99> with closing bracket ending at (line 1 column 417)"

The tree file I'm using as the input is here:

((Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,((((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),(((Schistosoma_mansoni,Echinococcus_multilocularis)),((((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis))),((((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis))))))))))))))root;

When I upload this file on iTOL, it plots it fine, and it seems like it works. I've tried to follow this same error posted on the Google Groups, but couldn't find a solution that works for me.

The full command is: 'iqtree -s cleaned.aln -B 1000 -alrt 1000 -T 100 -g limited_constrained_tree.txt'

I'm quite new to tree reading and understanding, and so I apologise if the issue is really straightforward, but would love some advice.

Best, kevin

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Heiko Schmidt Vienna, Austria

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Email: heiko.schmidt(AT)univie.ac.at Tel. : ++43 +1 / 4277 - 74321 http://www.cibiv.at/

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Email: heiko.schmidt(AT)univie.ac.at Tel. : ++43 +1 / 4277 - 74321 http://www.cibiv.at/

mickey-spongebob commented 2 years ago

Dear Heiko,

Apologies for the late reply. I was testing a few other things and got carried away. Very briefly, the problem is that I'd like to use a relatively well accepted phylogeny to then infer gene gain-loss. I've tried to use my own tree from the genomic data, and the trees are very inconsistent with well accepted ideas of animal evolution e.g. Streblospio is the sister group to all other animal, or some other annelids are misplaced in other animal lineages...

That's why I opted for using a fixed tree, in hopes that I could get additional support information for each branch. I actually managed to use the same tree to run successfully, except that I deleted the first and last bracket, meaning that the tree looks like this:

"(Monosiga_brevicollis,(Mnemiopsis_leidyi,(Amphimedon_queenslandica,(Trichoplax_adhaerens,(((Clytia_hemisphaerica,Hydra_vulgaris),((Actinia_tenebrosa,Nematostella_vectensis),Stylophora_pistillata)),(((Ciona_intestinalis,((Mus_musculus,Homo_sapiens),Danio_rerio)),Branchiostoma_floridae),(((Penaeus_vannamei,Daphnia_pulex),(Drosophila_melanogaster,Aedes_aegypti)),((Schistosoma_mansoni,Echinococcus_multilocularis),(((Lottia_gigantea,Octopus_vulgaris),(Crassostrea_gigas,Mizuhopecten_yessoensis)),(((Dimorphilus_gyrociliatus,((Streblospio_benedicti,(Helobdella_robusta,Capitella_teleta)),Platynereis_dumerilii)),Owenia_fusiformis),(Lingula_anatina,Phoronis_australis)))))))))));"

The subsequent tree result is actually quite different from this tree suggesting that maybe the issue is with the alignment (maybe).

(Streblospio_benedicti:0.4210851522,((((((((Aedes_aegypti:0.3865063759,Drosophila_melanogaster:0.5209781347)100/100:0.3652571158,Daphnia_pulex:0.6573762339)0/100:0.0631300242,Penaeus_vannamei:0.6683204615)100/100:0.1733150737,(Echinococcus_multilocularis:0.7879188107,Schistosoma_mansoni:0.6560005930)100/100:0.9062200965)0/99:0.0819962593,(((((Actinia_tenebrosa:0.2575000412,Nematostella_vectensis:0.2798540403)100/100:0.1221736669,Stylophora_pistillata:0.3735039455)100/100:0.2025877278,(Clytia_hemisphaerica:0.4366092489,Hydra_vulgaris:0.4863683183)100/100:0.5060512326)100/100:0.1042438251,(((Monosiga_brevicollis:1.5390575093,Mnemiopsis_leidyi:1.3180677373)100/100:0.1061921538,Amphimedon_queenslandica:1.0121545921)100/100:0.0931097535,Trichoplax_adhaerens:0.9010874882)100/100:0.0703759937)100/100:0.1440921496,(Branchiostoma_floridae:0.4888746227,(Ciona_intestinalis:0.9599043531,(Danio_rerio:0.2864267487,(Homo_sapiens:0.0595936516,Mus_musculus:0.0636346364)100/100:0.2392813549)100/100:0.2958589301)100/100:0.0661548281)100/100:0.0704359393)100/100:0.0728209434)100/100:0.0802888935,((((Crassostrea_gigas:0.3831265029,Mizuhopecten_yessoensis:0.3437519807)100/100:0.1066228466,Lottia_gigantea:0.4702467058)0/100:0.0497571030,Octopus_vulgaris:0.6052306382)100/100:0.0938041029,((Lingula_anatina:0.4135984138,Phoronis_australis:0.4744223066)100/100:0.0468119629,Owenia_fusiformis:0.4624031598)100/100:0.0350051565)0/70:0.0271085894)100/100:0.0626776942,(Dimorphilus_gyrociliatus:0.8142631553,Helobdella_robusta:0.8617469282)0/100:0.0899680731)100/100:0.0354893619,Platynereis_dumerilii:0.4437092033)100/100:0.0577168683,Capitella_teleta:0.4708102026);

I did have 2 additional sequences in the alignment file that were not in the constrain tree, but I've since removed them.

I notice that for all my runs, I see the following:

" Reading constraint tree limited_constrained_tree.txt... WARNING: Rooted constraint tree will be treated as unrooted tree "

Is it possible to make the rooted constraint tree be read as just that and then to see how well supported the tree is based on the alignment?

It seems that this isn't an IQTREE issue however, and just an alignment error.

Sorry for the trouble and thank you for all your help :-)

Of course any further advice is welcome but I'm also very grateful for all that you've shared thus far!

Best, kevin