Hi Karishma,

there are several program that you might want to use. Can you give a short example of these numeric values or further specify these variables? Or maybe name the file format that you like to work on?

Best

Sebastian

Hi Karishma,

You can use several software according to your data. If you want to infer a phylogeny based on your data, I think that you could to arrange your data in a matrix of distance (differences between measures of each pair - maybe a good point to start). You can try MEGA or PAUP to do that and perhaps compare topologies from different variables. However, if you want investigate hypothesis of trait evolution on known phylogenies I recommend BaTS (http://evolve.zoo.ox.ac.uk/evolve/BaTS.html) and BayesTraits programs (http://www.evolution.rdg.ac.uk/BayesTraits.html).

Probably, there is a good package in R-project that smooth your job.

Best,

Caio

Karishma

yes it is would be very convenient if you can tell what kind of file formats you are comfortable with and what type of data you are using. As others have specified R is a good option but you can do it with mesquite also. But if you can be a little more elaborate about the data and what you want to do it would be easier to find the tool.

Best

Niladri

I think you want to simply list the data in a heirarchical manner according to some predetermined phylogenetic order. To do this, just make a spreadsheet of the taxa, and list the data in columns, then arrange the taxa according to whatever order you agree with in the literature.

OR ask your question again in a more clear manner.

Maybe I don't understand your issues well enough, but it sounds to me like MacClade (http://macclade.org/macclade.html) would handle this. Here too, you'd import the tree in Newick format from any source you like. The data would be in tabular format of taxa versus characters with character states filling the blocks. Then MacClade would allow you to visualize all data in phylogenetic context, reconstruct ancestral states, and many more ways.

If I were to do this (and I haven't), I would try the Bayesian approach (causal hypothesis). Caio gives some great links above.

Isn't the Bayesian approach being discussed referring to methods for constructing phylogeny from these characteristic states? This doesn't seem to me to be the stated goal, but again, maybe I'm misunderstanding.

If I understand the goal, using MacClade as Jeffrey describes would do the trick. To work on how such traits evolve, look further at Felsenstein's contrasts.

hey. May be you can try Phylogeny.fr. It is available free online....

Hi Karishma

I will suggest if you could read out the following article, I think your problem seems to be similar to this one. http://www.academicjournals.org/ajb/PDF/pdf2009/1Dec/Hayat%20et%20al.pdf

Hi Karishma,

as dr Zander said, your question is maybe not clear enough... If you keep you data in excel format (as I do when I am working with non nucleotide and non proteine sequence data) you can not arrange it in phylogenetic order (or I do not know how). For that you will need someone to make you real data base (SQL). My opinion is that the quickest solution is just to make sure to have the same names for species in native excel file and tree that represents phylogenetic relations. You have to decide what analyses you want to do (map variables on a tree or infer phylogeny from it) and according to that decide what software you will use and how to prepare input files (tree and raw data).

Cheers!

our data is in excel format which consists of simple numeric values. i tried exploring ape pacakage. but iwas facing some problem with retrieval of trees from treebase.

Also how can one 'map variables on a tree or infer phylogeny from it'?

Huh…

As many people here said, you can do several main things with your non nucleotide data:

1. investigate hypothesis of trait evolution (that means that you have to have “molecular tree” and you map your traits to see if you have phylogenetic signal in it (closely related species tend to be more similar to one another than expected by chance) or simple said, how traits evolve along tree.

2. Infer phylogenetic tree from non nucleotide data (you get “non molecular tree”) and you can compare it with “molecular tree” for instance.

3. Do comparative study of several species using those non nucleotide data. For that you have to check do you have phylogenetic relatedness on your data. If you have it that you have to do all comparative analyses on “corrected data set”. Using this method you can account for similarities due to common ancestor and recognize similarities that are due to living in same environment for instance.

Story become more complicated when you take into account what kind of data you have (continuous or discrete)…

Sorry if I am not clear enough, English is always a small barrier for me :)

You can find plenty literature for all I mentioned... for now I did not go into technical details how to do it, just wanted to present overall picture what you can do with your data...

Cheers!

Tanja.

sorry for spelling and other mistakes, I do not read my lines after I finished it :) hope you will understand it...

Thats alright.:)

I am trying with the ape package. that seems to be great. besides i am on the exploring stage. thanks for suggestions.

also i would ask again if i face problems with ape as i am not from a true computational biology background.

Hi Caio,

The links you provided didnot open. i guess there is some problem with it.

Hi Karishma,

I think that Research Gate isn't redirecting links very well. You could to google Bayes Traits Pagel and BaTs Parker.

Ok. I will try that. Thanks

use NTSys software: First make Data sheet in Excel with 0 for absence and 1 for presence of the character and then use the software to make Dandrogram and similarity Matrix.