Phylogenetic Analysis

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Questions related to Phylogenetic Analysis

How can I get Genbank accession code given the scientific names?

Hello! I now have a complete list of about 23k plant species that I want to check if Genbank has the sequencing data for a phylogenetic analysis later, and I am really new to the topic. Is...

03 November 2020 4,621 3 View

Anyone working on Molecular Taxonomy?? I would be highly obliged if anyone could help me with primer selection and Phylogenetic analysis ??

I have a wide range of freshwater microalgae collected from various districts of Tamil Nadu. I am looking for a collaborator who could help me with molecular identification of some rare unknown...

24 September 2020 8,172 1 View

What are the best conditions for preserving long-term feces samples for phylogenetic analysis?

Hello all, I am trying to obtain information about the specific conditions for the method of preserving feces samples for mammals ( preservative type, preservative concentrate, preservation...

24 August 2020 7,284 10 View

What would serve as the best outgroup for proteobacteria?

I am conducting a phylogenetic analysis on LuxR solo of alpha, beta and gammaproteobacteria. I am building three separate trees for each. What would serve as the best outgroup in all three trees?

15 August 2020 2,846 2 View

Why are the ClustalW (codon) and MUSCLE (codon) alignment options greyed out in MEGA-X?

Hi, I'm currently trying to do a multiple sequence alignment for a gene family using the coding nucleotide sequences. I want to create an alignment based on the amino acid sequences but that is...

29 July 2020 2,968 3 View

How many references sequences should use for a phylogenetic tree construction?

I have identified fungus isolates from the fruit surface by SSU +ITS+ LSU regions, such as : 1) Fusarium kyushuense , 2) Fusarium proliferatum ;3) Aspergillus aculeatus ;4) Aspergillus europaeus...

16 July 2020 5,734 2 View

Which genetic marker (nuclear DNA) should I use for phylogenetic analysis of fish?

I am studying two types of Ophidiid fishes having features morphologically similar and would like to genetically classify them. I have already investigated COI region of mtDNA, but the genetic...

15 July 2020 7,768 7 View

What is cophenetic correlation?

What is cophenetic correlation coefficient and how is it computed for a clustering method. Also how can it be used to compare two different distance matrices?

28 April 2020 1,961 1 View

Can I Combine Data and Tree Information into One Tree in Mesquite?

Is it possible to enter two different types of information into Mesquite? I have two sets of species data: the divergence times (in millions of years) i.e. how old each species is and the...

23 March 2020 6,495 3 View

What is the best way to date a phylogenomic tree?

What is the best way to date a phylogenomic tree using fossil calibration? It is more or less straightforward with a few Sanger loci using programs like BEAST, but it becomes intractable with...

27 February 2020 4,395 8 View

Which software can be used to prepare nexus file for phylogenetics analysis in Mr Bayes?

which software can be used to prepare nexus file for phylogenetics analysis in Mr Bayes? which format is best interleaved or sequential formats? Can you please explain?

23 February 2020 5,044 3 View

What are the best molecular markers for phylogenetic analysis of Metazoa?

I would like to know if there is any literature on the genes that are considered the best molecular markers for phylogenetic analysis on the Metazoa scale.

29 December 2019 1,308 2 View

How do you combine multiple SEQ files iinto one file (FASTA or notepad)?

I use MEGA X for my phylogenetic analysis and sometimes I may work with 70+ sequences. If any of you know a method that can combine these sequences into one and free me from the ////tedious////...

01 August 2019 3,173 3 View

BaysTraits analysis: Using random sample of trees or most probable trees?

Hello. I want to run an MCMC analysis on BayesTraits using a set of Bayesian trees I created using MrBayes. I want to run the analysis using both the consensus tree and a sample of 1,000 trees to...

29 July 2019 6,135 2 View

What details should be followed in MEGA-X for the Multiple Sequence Alignment of 16S data?

I have some 16S RNA sequence with which I want to do the phylogenetic analysis, so Initially I did BLAST against SILVA db and NACBI 16S db and went for MSA in MEGA-X using Muscle and Clustal both...

22 July 2019 9,495 3 View

Anyone know how to concatenate several protein sequences for phylogenetic analysis?

17 July 2019 5,576 2 View

Is it good to strip gaps in a protein MSA file for phylogenetic analysis?

I'm analyzing 445 protein sequences of a single protein for phylogenetic analysis. Multiple sequence alignment of these sequences is showing gaps of different sizes. Is it ok to keep these gaps...

29 April 2019 1,202 3 View

I was only able to generate forward sequences for some of my matK, rbcL and ITS1 genes and will they still be useful for my phylogenetic analysis?

I sent some plant DNA for DNA sequencing and apparently, though sequences were sent back, some pairs don't create a consensus sequence. The sequencing company tried to re-sequence, bu to no...

27 April 2019 2,805 4 View

Why am I receiving node ages in some strange units instead of millions of years using BEAST?

While running fossil-calibrated molecular-clocks analysis in BEAST, I keep receiving some strange numbers as node ages. I input the numbers in millions of years (see Fig.1) and yet I am receiving...

17 April 2019 9,946 6 View

How to obtain stat. support for a certain hard clade when a set of phylogenetic trees is given?

I have a set of trees (e.g., MrBayes output *.runX.t) with many taxa: A, B, C, .... Z. I need to infer statistical support for a certain clade ((E,F),G). Sumtrees (Dendropy package) is a useful...

31 March 2019 8,779 4 View

Should I remove my outgroup sequences when testing for the best substitution model in PartitionFinder?

Hello, Can anyone help me to argument wheter I shoul or not remove my outgroup sequences before running a substitution model test (PartitionFinder)? I have heard that it is a best practice to...

18 March 2019 4,048 3 View

Phylogenetic analysis verses Single stranded confirmatory polymorphism (SSCP)?

please what are the differences between phylogenetic analysis and SSCP in genetic diversity/variation of an organism?

01 February 2019 1,625 2 View

Why is BAMM producing strange results with hundreds of identified rate shifts?

Hi, I am running BAMM on different Newick-format chronograms. While all other trees run perfectly fine, I am getting some strange results when using one particular tree. This tree originally had...

10 January 2019 6,933 2 View

How to interpret branch support values on phylogenetic trees?

Hi, I generated the phylogenetic tree below with PhyML (Approximate Likelihood-Ratio Test: SH-like) at www.phylogeny.fr. I have read that support values indicate the degree to which one can be...

04 January 2019 4,881 3 View

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