Phylogenetic Analysis

Exchange knowledge in the field of molecular systematics, phylogenetic reconstruction and their application to systematics, biogeography and... | Contact experts in Phylogenetic Analysis to get answers

2,001 views 531 posts

Questions related to Phylogenetic Analysis

What is the standard way of preparing homolog sequences for a phylogenetic analysis?

I have two protein sequences with around 50% identity between them. I want to study the phylogenetic relationship between them. I came up with a method myself: Step 1: blast each of the sequences...

12 November 2018 3,628 2 View

BEAST: Real long branches causing negative branch lengths?

Hi everyone. I am trying to date the divergence of Cuscuta from the rest of Convolvulaceae using the BEAST software package. Cuscuta is a parasitic lineage and therefore many of the generally...

06 November 2018 1,847 4 View

Is there a lower limit for number of bases included in a phylogenetic analysis, and what is the best way to handle varying sequence length?

I have a set of HIV pol sequence data, and after alignment it is clear that some sequences are much shorter than others – primarily due to sequencing issues. Because the gaps/missing data are not...

05 September 2018 2,393 4 View

What are the major differences between the use of molecular data and morphological data and how is analysis and interpretation of the data impacted?

id like to know the similarities and differences of using morphological data vs molecular data for compiling a data matrix and conducting a phylogenetic analysis

09 June 2018 6,695 4 View

How can I calculate dN/dS within and between species?

0 📷 9 hours ago by krc3004 • 0 Recently I have been very interested in calculating the dN/dS ratio to estimate rates of nonsynonymous and synonymous substitutions. Since I've just...

28 May 2018 4,264 3 View

What is the best procedure for sequencing bacteria in phylogeny analysis?

What is the best procedure for sequencing bacteria in phylogenetic analysis. Using isolated plasmid DNA from the bacterial cells and adding omto the primer (27F and 1492R) or just taking the...

11 April 2018 7,792 6 View

What is the most efficient way for fungal DNA extraction?

The protocol must be able to obtain DNA from bracket fungi.

10 April 2018 6,229 5 View

¿Are there a recent tutorials of BEAST2 and BEAUti?

Hello everyone! I have been consulting this webpage http://beast.community/ and http://www.beast2.org/ , but the examples for the use of BEAUti and BEAST are for old versions. The versions of...

03 April 2018 4,092 3 View

I'm looking for review articles focused Euphorbiaceae-fungal endophytes interactions ?

I'm looking for review articles which are focused on the phylogenetic analysis of South african (even madagascar island) Euphorbiaceae in relation to endophytic fungi hosted in theses phytotaxa

16 January 2018 4,523 3 View

Can somebody recommend me free software for sequences phylogenetic analysis, which can process large dataset?

I have large amount of separate organisms sequences (over 1500), but I can't process it by using Mega, Genome Workbench, Seaview...

01 January 2018 3,309 4 View

How do I report a new fungal species?

How do I report a new fungal species? If after DNA sequencing (ITS) and phylogenetic analysis I strongly suspect my fungal isolate is a new species that differs completely from previous species...

03 December 2017 8,911 6 View

How to statistically calculate the number of ML/BI trees required for a phylogenetic analysis?

I am currently doing a phylogenetic analysis for a species of virus having many subtypes (Human papillomavirus) for around 100 whole genome specimen and 50 partial sequences belonging to ~6...

02 December 2017 8,267 2 View

Can someone suggest any govt/private lab where DGGE facility is available with experts handling it? And what are the charges?

I want to analyze the culturable as well as unculturable bacterial diversity present in soil samples. For this, I need to carry out DGGE of those soil samples followed by phylogenetic analysis by...

07 November 2017 8,800 2 View

What are common issues faced in MSA building especially for use in Phylogenetics?

A phylogeny is only as good as the alignment it is built on. When comparing generated sequence data with publicly available data (ie NCBI) there seems to be a variety of problems that can arise....

28 October 2017 9,659 3 View

How could I confirm species endemism using DNA barcoding and/or phylogenetic analysis?

Hello everybody, I am working with one endemic plant species. I managed to get sequences from two loci. I would like to know how to assess the endemism of that plant species using those two...

24 October 2017 2,123 7 View

How to remove redundant and incomplete protein sequences during multiple sequence alignment and phylogenetic analysis?

I want to eliminate redundant and incomplete sequences from my PSI-BAST result of a protein for multiple sequence alignment and phylogenetic analysis. Kindly suggest how to do it.

08 October 2017 1,838 4 View

How many sequences it needed to put in a crown group to calibrate a tree?

I want to date some clades found from a phylogenetic analysis of a complex species. The calibration point is on the stem, between my complex species and a sister genera. After using some sister...

18 August 2017 4,289 2 View

Why the scale bar greyed out in Mega 5.0 when making a phylogenetic tree?

Hi, everyone. I've been trying to generate a bacterial 16S rRNA phylogenetic tree with a scale bar. I selected NJ, 1000 bootstrap, and I got original tree and bootstrap concensus tree. By clicking...

05 August 2017 9,955 3 View

Why the scale bar greyed out in Mega 5.0 when making a phylogenetic tree?

Hi, everyone. I've been trying to generate a bacterial 16S rRNA phylogenetic tree with a scale bar. I selected NJ, 1000 bootstrap, and I got original tree and bootstrap concensus tree. By clicking...

05 August 2017 668 3 View

How to simply collapse branches on phylogenetic tree?

I have a phylogenetic tree containing approx. 2000 sequences. From those I have a selection of approx. 200 sequences. To visualize their distribution, I would like to "select" those 200 sequences...

06 July 2017 4,058 7 View

How do I construct a phylogenetic tree?

Good day everyone, I am to construct a phylogenetic tree with proteins but some of the homologs of the protein I am working with are truncated. How do I deal with these?

02 July 2017 5,862 4 View

Why a morphological data appeared in-congruent with all molecular data( sequenced data )during phylogenetic analysis ?

Reasons behind the in-congruence in plant genera based on taxonomy and evolution?

27 June 2017 6,858 3 View

How can I statistically analyse numbers/types of ancestral character states in R?

I am currently reconstructing ancestral character states in R. I have looked everywhere but cannot find out which statistical analyses I could/should run on R to quantify my results against time?...

19 June 2017 5,580 2 View

How to interpret the GMYC model results for species delimitation?

Dear all, I have a couple of questions regarding the GMYC model and its implementation. First of all, I am applying the model similarly to Humphreys and Barraclough (2014), trying to identify...

05 June 2017 294 2 View

Badges
Science method