I need to perform large-scale phylogenetic analysis of big dataset of GPCR sequences selecting as the input only residues involved in the ligand-binding site of those receptors (taken from the structural data) from the input multiple-sequence alignment. I wounder what method for phylogenetic trees calculation will be best (neighbourhood joining or pairs-distance calculations) for my task as well as how to make selection of the selecting residues properly (previously I’ve done it by cntrl-left click on the bottom of the alignment marking corresponded zone by red colour). On what additional details should I paid my attention during such calculations in case when I’m dealing with a very big number of sequences?
Then, you can use Jalview to select manually the ligand-binding domain in your alignment.
You can also use TrimAl to select only well aligned position that corresponding to phylogenetic signal. http://trimal.cgenomics.org/
For producing the tree on very big alignments, I would recommend FastTree. It produces quite good results and is very easy to use: http://www.microbesonline.org/fasttree/
thank you very much for the explanation!
I’ve already used TrimAl as the part of the Phylemon2 server and found it very useful
Regarding calculating Trees in JalView using subset of the residues: as I noticed the tree are calculated just in case when the positions of ligand-contacting residues are marked by red color in the top, aren’t it? Is it possible in addition to check on what exactly subset trees has been calculated based on the output results?
Finally regarding accuracy of the calculation of the trees- what method should produce best results for the alignment consisted of several hundred of sequences?
Then, you can use Jalview to select manually the ligand-binding domain in your alignment.
You can also use TrimAl to select only well aligned position that corresponding to phylogenetic signal. http://trimal.cgenomics.org/
For producing the tree on very big alignments, I would recommend FastTree. It produces quite good results and is very easy to use: http://www.microbesonline.org/fasttree/
I need to perform large-scale phylogenetic analysis of big dataset of GPCR sequences selecting as the input only residues involved in the ligand-binding site of those receptors (taken from the structural data) from the input multiple-sequence alignment. I wounder what method for phylogenetic trees calculation will be best (neighbourhood joining or pairs-distance calculations) for my task as well as how to make selection of the selecting residues properly (previously I’ve done it by cntrl-left click on the bottom of the alignment marking corresponded zone by red colour). On what additional details should I paid my attention during such calculations in case when I’m dealing with a very big number of sequences?
Thank you for the help,
James
_______________________________________________
Jalview-discuss mailing list
[Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)
thank you very much for the explanation!
I’ve already used TrimAl as the part of the Phylemon2 server and found it very useful
Regarding calculating Trees in JalView using subset of the residues: as I noticed the tree are calculated just in case when the positions of ligand-contacting residues are marked by red color in the top, aren’t it? Is it possible in addition to check on what exactly subset trees has been calculated based on the output results?
Finally regarding accuracy of the calculation of the trees- what method should produce best results for the alignment consisted of several hundred of sequences?
Then, you can use Jalview to select manually the ligand-binding domain in your alignment.
You can also use TrimAl to select only well aligned position that corresponding to phylogenetic signal. http://trimal.cgenomics.org/
For producing the tree on very big alignments, I would recommend FastTree. It produces quite good results and is very easy to use: http://www.microbesonline.org/fasttree/
I need to perform large-scale phylogenetic analysis of big dataset of GPCR sequences selecting as the input only residues involved in the ligand-binding site of those receptors (taken from the structural data) from the input multiple-sequence alignment. I wounder what method for phylogenetic trees calculation will be best (neighbourhood joining or pairs-distance calculations) for my task as well as how to make selection of the selecting residues properly (previously I’ve done it by cntrl-left click on the bottom of the alignment marking corresponded zone by red colour). On what additional details should I paid my attention during such calculations in case when I’m dealing with a very big number of sequences?
Thank you for the help,
James
_______________________________________________
Jalview-discuss mailing list
[Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)
From: jalview-discuss-bounces@jalview.org [mailto:jalview-discuss-bounces@jalview.org] On Behalf Of James Starlight
Sent: 06 November 2014 10:10
To: rstuder; jalview-discuss@jalview.org
Subject: Re: [Jalview-discuss] Phylogenetic trees calculated for specified alignment zones
also I'll very thankful if someone suggest me some server for the simple comparison of 2 phylogenetic trees and cluster calculations
Romain and Andreas have provided some great suggestions. I thought it worth adding that when using Jalview with web sites and other tools - the most convenient way to prepare selections for input (e.g. to a tree calculation) is by creating a new view (Ctrl or Command + T), select all the columns you want to employ for calculation and use the ‘View->Hide->All but selected region’ to hide everything that you do not want to employ for the tree calculation (shift+CMD/CTRL + H). Creating a view minimises the number of additional windows you create containing the same alignment data, and the input data view can be given it’s own name and archived in a jalview project. Once you have some results from the other tools, you can then add them the view, and explore the alignment further via Jalview’s subfamily shading methods (or even the Sequence Harmony service since its designed to predict functional site variation based on a set of defined subgroups on the alignment).
If you have any problems exporting alignment data from Jalview or importing the trees back in to Jalview from RaxML or FastTree, send an email ! We also now have PHYLIP format input/export support in the development versions of Jalview which is useful when working with RaxML.
Jim.
PS. Just to expand on Romain’s comment about accuracy: Jalview’s tree algorithms are rigorous but relatively primitive, and not considered appropriate for general phylogenetic analysis tasks. Also, Jalview doesn’t provide support for model selection (picking the right model to calculate the intersequence distances from the alignment) or bootstrapping (identifying the statistically significant branches in the tree). FastTree and RaxML both employ heuristic maximum likelihood searches to produce an accurate tree more quickly and includes approximate support calculations.
Thank you very much for the suggestions!
I’ll try to use another software to calculate the trees!
Indeed I’ve noticed that trees produced by Jalview often consist of the wrong distributions and grouping of sequences especially in case when it has been made for big number of sequences put in alignment. It’s also strange that I’ve obtained better trees in case of the faster method (distance averaging using Blosum matrix) in comparison to more accurate neighbor joining algorithm.
Romain and Andreas have provided some great suggestions. I thought it worth adding that when using Jalview with web sites and other tools - the most convenient way to prepare selections for input (e.g. to a tree calculation) is by creating a new view (Ctrl or Command + T), select all the columns you want to employ for calculation and use the ‘View->Hide->All but selected region’ to hide everything that you do not want to employ for the tree calculation (shift+CMD/CTRL + H). Creating a view minimises the number of additional windows you create containing the same alignment data, and the input data view can be given it’s own name and archived in a jalview project. Once you have some results from the other tools, you can then add them the view, and explore the alignment further via Jalview’s subfamily shading methods (or even the Sequence Harmony service since its designed to predict functional site variation based on a set of defined subgroups on the alignment).
If you have any problems exporting alignment data from Jalview or importing the trees back in to Jalview from RaxML or FastTree, send an email ! We also now have PHYLIP format input/export support in the development versions of Jalview which is useful when working with RaxML.
Jim.
PS. Just to expand on Romain’s comment about accuracy: Jalview’s tree algorithms are rigorous but relatively primitive, and not considered appropriate for general phylogenetic analysis tasks. Also, Jalview doesn’t provide support for model selection (picking the right model to calculate the intersequence distances from the alignment) or bootstrapping (identifying the statistically significant branches in the tree). FastTree and RaxML both employ heuristic maximum likelihood searches to produce an accurate tree more quickly and includes approximate support calculations.
On 06/11/2014 09:35, rstuder wrote:
Yes, trees in Jalview are calculated only based on marked positions.
For accuracy, I would not use phylogenetic tools from Jalview.
I would rather do the following:
Select the positions in Jalview.
Copy them.
Paste them as new alignment.
Save the alignment in a new file.
And then I use FastTree or RAxML (or even PhyML if you have access to good computer cluster).
Romain
On 05/11/2014 20:18, James Starlight wrote:
Hi Romain,
thank you very much for the explanation!
I’ve already used TrimAl as the part of the Phylemon2 server and found it very useful
Regarding calculating Trees in JalView using subset of the residues: as I noticed the tree are calculated just in case when the positions of ligand-contacting residues are marked by red color in the top, aren’t it? Is it possible in addition to check on what exactly subset trees has been calculated based on the output results?
Finally regarding accuracy of the calculation of the trees- what method should produce best results for the alignment consisted of several hundred of sequences?
Then, you can use Jalview to select manually the ligand-binding domain in your alignment.
You can also use TrimAl to select only well aligned position that corresponding to phylogenetic signal. http://trimal.cgenomics.org/
For producing the tree on very big alignments, I would recommend FastTree. It produces quite good results and is very easy to use: http://www.microbesonline.org/fasttree/
I need to perform large-scale phylogenetic analysis of big dataset of GPCR sequences selecting as the input only residues involved in the ligand-binding site of those receptors (taken from the structural data) from the input multiple-sequence alignment. I wounder what method for phylogenetic trees calculation will be best (neighbourhood joining or pairs-distance calculations) for my task as well as how to make selection of the selecting residues properly (previously I’ve done it by cntrl-left click on the bottom of the alignment marking corresponded zone by red colour). On what additional details should I paid my attention during such calculations in case when I’m dealing with a very big number of sequences?
Thank you for the help,
James
_______________________________________________
Jalview-discuss mailing list
[Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)
Finally regarding FastTree utility I’ll be very thankful if someone provide me with the ideas of how to improve accuracy of the trees (e.g using bootstrap or thx else) produced by its.
On default I’m using fasttree -n 10 hOR_multipleAlignments.fa > tree_fast_allSEQ.ph
providing only flag for bootstrap in additional to standart input.
Thank you very much for the suggestions!
I’ll try to use another software to calculate the trees!
Indeed I’ve noticed that trees produced by Jalview often consist of the wrong distributions and grouping of sequences especially in case when it has been made for big number of sequences put in alignment. It’s also strange that I’ve obtained better trees in case of the faster method (distance averaging using Blosum matrix) in comparison to more accurate neighbor joining algorithm.
Romain and Andreas have provided some great suggestions. I thought it worth adding that when using Jalview with web sites and other tools - the most convenient way to prepare selections for input (e.g. to a tree calculation) is by creating a new view (Ctrl or Command + T), select all the columns you want to employ for calculation and use the ‘View->Hide->All but selected region’ to hide everything that you do not want to employ for the tree calculation (shift+CMD/CTRL + H). Creating a view minimises the number of additional windows you create containing the same alignment data, and the input data view can be given it’s own name and archived in a jalview project. Once you have some results from the other tools, you can then add them the view, and explore the alignment further via Jalview’s subfamily shading methods (or even the Sequence Harmony service since its designed to predict functional site variation based on a set of defined subgroups on the alignment).
If you have any problems exporting alignment data from Jalview or importing the trees back in to Jalview from RaxML or FastTree, send an email ! We also now have PHYLIP format input/export support in the development versions of Jalview which is useful when working with RaxML.
Jim.
PS. Just to expand on Romain’s comment about accuracy: Jalview’s tree algorithms are rigorous but relatively primitive, and not considered appropriate for general phylogenetic analysis tasks. Also, Jalview doesn’t provide support for model selection (picking the right model to calculate the intersequence distances from the alignment) or bootstrapping (identifying the statistically significant branches in the tree). FastTree and RaxML both employ heuristic maximum likelihood searches to produce an accurate tree more quickly and includes approximate support calculations.
On 06/11/2014 09:35, rstuder wrote:
Yes, trees in Jalview are calculated only based on marked positions.
For accuracy, I would not use phylogenetic tools from Jalview.
I would rather do the following:
Select the positions in Jalview.
Copy them.
Paste them as new alignment.
Save the alignment in a new file.
And then I use FastTree or RAxML (or even PhyML if you have access to good computer cluster).
Romain
On 05/11/2014 20:18, James Starlight wrote:
Hi Romain,
thank you very much for the explanation!
I’ve already used TrimAl as the part of the Phylemon2 server and found it very useful
Regarding calculating Trees in JalView using subset of the residues: as I noticed the tree are calculated just in case when the positions of ligand-contacting residues are marked by red color in the top, aren’t it? Is it possible in addition to check on what exactly subset trees has been calculated based on the output results?
Finally regarding accuracy of the calculation of the trees- what method should produce best results for the alignment consisted of several hundred of sequences?
Then, you can use Jalview to select manually the ligand-binding domain in your alignment.
You can also use TrimAl to select only well aligned position that corresponding to phylogenetic signal. http://trimal.cgenomics.org/
For producing the tree on very big alignments, I would recommend FastTree. It produces quite good results and is very easy to use: http://www.microbesonline.org/fasttree/
I need to perform large-scale phylogenetic analysis of big dataset of GPCR sequences selecting as the input only residues involved in the ligand-binding site of those receptors (taken from the structural data) from the input multiple-sequence alignment. I wounder what method for phylogenetic trees calculation will be best (neighbourhood joining or pairs-distance calculations) for my task as well as how to make selection of the selecting residues properly (previously I’ve done it by cntrl-left click on the bottom of the alignment marking corresponded zone by red colour). On what additional details should I paid my attention during such calculations in case when I’m dealing with a very big number of sequences?
Thank you for the help,
James
_______________________________________________
Jalview-discuss mailing list
[Jalview-discuss@jalview.org](mailto:Jalview-discuss@jalview.org)
[http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss](http://www.compbio.dundee.ac.uk/mailman/listinfo/jalview-discuss)
