Phylogenetic Analysis

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Questions related to Phylogenetic Analysis

How many samples must be recorded for the evaluation of genetic diversity of half sib families in pot experiment?

How many samples must be record for evaluation genetic diversity of half-sib families in pot experiment? I want to know the minimum number of records for each family to calculate general combining...

07 March 2015 9,305 5 View

What are the molecular identification methods used for fungi?

I had studied that internal transcribed spacer (ITS), Isolation of DNA and PCR amplification and DNA sequencing and BLAST and phylogenetic analysis are used. Can anyone suggest articles about...

04 March 2015 5,370 8 View

What is the best phylogenetic program to yield reasonable analysis from morphological data?

I have data (morphological data) that characterizes tumor in different patients and would like to run a phylogenetic analysis on it. What is the most effective and user-friendly program that I can...

03 March 2015 2,972 15 View

Anyone who can help me with the divergence time estimation using BEAST?

Hi, I have tried BEAST for calculating the evolutionary divergence time for my study, consisting of ~ 80 taxa & having a length of ~80,000 bps per taxa. After the run was completed, the BEAST...

03 March 2015 9,872 6 View

In comparing the two different species from the same family, would it make sense to include an out-group in the phylogeny tree?

I am working with trematode parasite and my main aim is to confirm the species using molecular approach and see our species is how close to the other reported similar species. I applied to...

03 March 2015 8,794 18 View

Prensently, what is the best software for phylogenetic analysis, including character traits and genome sequence ?

I am looking for a software, quite user friendly, for character data and genomic sequence. It should be didactic and help for learning phylogenetic analysis. I look at Mesquite but it seems...

03 March 2015 4,806 2 View

How many samples must be recorded for the evaluation of genetic diversity of half sib families in pot experiment?

How many samples must be record for evaluation genetic diversity of half-sib families in pot experiment? I want to know the minimum number of records for each family to calculate general combining...

03 March 2015 1,477 6 View

What are the molecular identification methods used for fungi?

I had studied that internal transcribed spacer (ITS), Isolation of DNA and PCR amplification and DNA sequencing and BLAST and phylogenetic analysis are used. Can anyone suggest articles about...

03 March 2015 2,030 9 View

Can anyone tell me please how to make a file of DNA sequences for Phylip software? And how do I proceed further with it?

I want to do phylogenetic analysis among DNA sequences of some plant species. I read the instructions in Phylip's manual and followed the instructions. I made a file in Phylip format...

03 March 2015 3,992 5 View

What is the purpose of misidentified or contaminated sequences in a dataset?

Hello In phylogenetic analysis: What is the purpose of misidentified or contaminated sequences in a data set? How can I remove this contamination? If I use a Neighbor-Joining algorithm (with a...

03 March 2015 1,796 4 View

Any suggestions on the inconsistency between blast and phylogenetic tree?

I did nearly full 16S sequencing (1382 bps) of my isolate. According to blast result in EZ taxon data base the isolate showed 98.5% similarity to Kocuria polaris but when I drew phylogenetic tree...

03 March 2015 9,825 13 View

Anyone who can help me with the divergence time estimation using BEAST?

Hi, I have tried BEAST for calculating the evolutionary divergence time for my study, consisting of ~ 80 taxa & having a length of ~80,000 bps per taxa. After the run was completed, the BEAST...

03 March 2015 5,291 5 View

What's the difference between aldoketo reductase and aldo-keto reductase?

I am looking for phylogenetic analysis is aldoketo reductase family protein, while searching the sequence related to the same in NCBI. Aldo-keto reductase and aldoketo reductase giving different...

23 February 2015 2,657 3 View

How to correct negative branches from neighbor-joining method?

I am getting negative branches with the Neighbor-joining method, which I set to zero. However, I've read that I should transfer negative distances somewhere else and I do not know how. Does...

23 February 2015 3,868 4 View

Does anyone have an idea about the phylogenetic analysis of SSR allelic data?

I have demonstrated a project, assessing the genetic diversity of breeds of an animal using SSR markers. I've got the allelic data from GeneMapperv.3.7 but i have no idea how to plot the...

17 February 2015 4,496 6 View

What textbook(s) on phylogenetic analysis would you recommend for undergraduates who want to learn the basics?

Ideally, such a textbook would include Maximum Likelihood, Maximum Parsimony, and BiSSE analyses

07 February 2015 8,291 23 View

Does anyone know if there is a R package to perform a Canonical Phylogenetic Ordination (CPO)?

As far as I know, the only software that allows you to make a CPO is CANOCO. I was wondering if there is a R package to make the same analysis or an equivalent. Thank you! EDIT: In case new...

05 February 2015 9,565 4 View

What's the difference between aldoketo reductase and aldo-keto reductase?

I am looking for phylogenetic analysis is aldoketo reductase family protein, while searching the sequence related to the same in NCBI. Aldo-keto reductase and aldoketo reductase giving different...

02 February 2015 4,355 3 View

What is the easiest way to create XML format files with the sequences and the tree in the same file?

I want to run an analysis and have to use XML-based file format which I have never done before. The guide tree and the sequences have to be in the same file. Does anybody know a program which can...

02 February 2015 7,702 5 View

What textbook(s) on phylogenetic analysis would you recommend for undergraduates who want to learn the basics?

Ideally, such a textbook would include Maximum Likelihood, Maximum Parsimony, and BiSSE analyses

02 February 2015 1,300 24 View

Does anyone have an idea about the phylogenetic analysis of SSR allelic data?

I have demonstrated a project, assessing the genetic diversity of breeds of an animal using SSR markers. I've got the allelic data from GeneMapperv.3.7 but i have no idea how to plot the...

02 February 2015 931 7 View

How can the RAPD protocol be refined apart from the optimization of various parameters?

Can RAPD be successfully coupled with other techniques?

02 February 2015 3,593 3 View

How can I compute Bayesian posterior probability for a given phylogenetic tree?

After a search for a suitable phylogenetic tree using RAxML, how can I compute the Bayesian posterior probability for the resulted tree. What programs shall I use? Thanks.

21 January 2015 6,718 11 View

From where can i get the best book (of keys) or pdf version for species level identification in nematodes for family Schistonchus and diplogastridae?

I am unable to get a book containing keys for identification of nematodes of Schistonchus and Diplogastridae family. If anyone can tell me where i can get either pdf version of the book or...

09 January 2015 6,351 1 View

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