Phylogenetic Analysis

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Questions related to Phylogenetic Analysis

How to choose the best fit evolutionary model based on jmodeltest analysis?

I am working on mtCOI sequences of whiteflies and aiming to do phylogeny based on that aligned sequences. I want to see the best fit of my sequences. However the jmodltest gives different models...

10 May 2017 5,004 7 View

I need program for phylogentic tree easily using more then MEGA6 ?

phylogentic tree, MEGA6

23 April 2017 4,522 7 View

Is the species identification by DNA barcoding gap through genetic distances calculated with a K2P model still reliable?

After the following two articles, I got confused and am trying to figure out whether the method of DNA barcoding gap to identify species is suitable or not. How should i treat this...

21 April 2017 4,887 4 View

Hello everyone, should we use Kakusan software for Bayesian analysis?

I have concatenated and converted fasta file of 2 genes using sequencematrix into nexus file (for mrbayes and MP PAUP) and Phylip (for online raxml). I just directly used my nexus in the Bayesian...

19 April 2017 4,649 3 View

Is there any phenotype database for Streptomyces?

I'm identifying my Streptomyces isolates at the specie level. I already performed all the phenotype / chemotaxonomic tests, and constructed a phylogenetic tree. However, I didn't find the...

17 April 2017 1,864 3 View

Polymorphism from ISSR markers

Does anybody have idea to determine polymorphic bands in a binary matrix (ISSR) and how to calculate the genotypes provided from each locus. I calculated the number of bands which present 0 and 1...

04 April 2017 7,074 6 View

During phylogenetic analysis, which one is more appropriate complete deletion, partial deletion or pairwise deletion?

Actually, I want to know the differences among them..

03 March 2017 8,374 3 View

What means the "bootstrap likelihood" in RAxML?

Hello. Please understand that i'm not proficient in English. I wonder the means of "bootstrap likelihood" in RAxML. I'm running ML+Rapid bootstrap for analysis settings, about 1428 taxa, DNA...

03 March 2017 635 1 View

Does any one know the command string used in paup for CI and RI values?

Does any one know the command string used in paup for CI and RI values? Using Cipres and need to add the command string to get CI and RI values.

03 March 2017 1,228 2 View

My phylogenetic tree topology is fine but the confidence (nodes bootstrap value) is quite less than the threshold. Do journals accepts such trees?

ML tree HCV NS5B sequences

03 March 2017 7,458 4 View

How can I calculate maximum and minimum tree length for a character under squared parsimony reconstruction?

I would like to calculate QVI (quantitative convergence index) for a set of continuous characters with ancestral states reconstructed under squared parsimony assumption. In order to do it I need...

02 February 2017 2,976 4 View

How to edit tip labels in MEGA?

I've created a number of phylogenetic trees in MEGA but I would like to edit the tip labels. To this point, I have not been able to find a way to do so. Your advice is appreciated.

02 February 2017 5,656 9 View

How to compute the fungal phylogenetic diversity by ITS2 sequencing?

The fungal ITS region varies roughly, with some exceptions, between approximately 450 and 750 base pairs (bp) in length. This feature makes it hard to compute the phylogenetic diversity. I used...

02 February 2017 5,921 14 View

Doing DNA barcoding with ITS2 in Quercus, and ML trees are not correctly grouping known clades together; however, NJ is. Specific reason for this?

I want the phylogeny to be as accurate as possible but RAxML is not giving correct groupings.

02 February 2017 3,225 2 View

MEGA6 Maximum Likelihood output meaning?

Hello Everyone, I am doing maximum likelihood trees for a set of sequences using the ITS rDNA gene and actin gene in a lichenised green alga. I understand bootstrapping, but I am not sure what the...

26 January 2017 4,634 3 View

Is it possible to remove just one node from a phylogenetic tree without actually making the tree again?

From the tree that i have I wanted to remove one of the nodes. is it possible to remove that node from the tree file?

01 January 2017 3,962 7 View

Which method is commonly used for relationship of plant species?

There are many methods used in phylogeny viz. Maximum Likelihood Tree; Neighbor-Joining Tree; Minimum evolution Tree; UPGMA TREE & Maximum Parsimony Tree. I have simply two questions Whats a...

01 January 2017 2,425 9 View

Same log likelihood values for site models in PAML?

Dear All, In CODEML, I am facing a problem with log likelihood values. I get exact values for M1 and M2 site models while nearly same values for M7 and M8 . I tried changing the parameters such as...

01 January 2017 7,667 2 View

All of my Beast statistic is good, except tmrca and branchRates which are showing OEO with ESS "-" ?

I am trying to run Beast 1.8.4 using two fossil calibrations of clouded leopard and Lion-Jaguar with tiger subspecies sequences. Under strict clock model with Yule process, my priors for clouded...

01 January 2017 9,671 3 View

MEGA6 Maximum Likelihood output meaning?

Hello Everyone, I am doing maximum likelihood trees for a set of sequences using the ITS rDNA gene and actin gene in a lichenised green alga. I understand bootstrapping, but I am not sure what the...

01 January 2017 915 4 View

Looking for insights into why two sequences don't cluster closely together on phylogenetic tree despite aligning with 99% identity and 97% querycover?

I used RDP classifier in my analysis pipeline of some mcrA amplicon data which assigned my OTU 1 the identity of a specific clone (MCR12). However, if I include that clone's mcrA sequence in my...

01 January 2017 9,995 6 View

How to interpret MLST analysis outputs?

Hello, I'm working on phylogenetic analysis of E.Coli and am using MLST to get more information about the evolutionary history. But I'm struggling to understand the ouputs of such an MLST...

28 December 2016 1,123 4 View

Which is the best method/algorithm for phylogenetic comparison of protein coding sequences (ORF) and amino acid sequences?

I need compare a particular protein coding (nucleotide) sequence and amino acid sequence with vertebrates and non-vertebrates and understand the mechanisms of evolution and relatedness using...

12 December 2016 3,498 3 View

How to calculate phylogenetic conservation?

Aim:Are the features that we are interested in more conserved in a set of virus strains than expected? Input:1) 100 virus genomes (strains of same virus) as pairwise aligned sequences (no MSA).2)...

12 December 2016 7,939 6 View

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