Phylogenetics

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Questions related to Phylogenetics

Are there any good tutorials or literature dealing with cluster analyses of categorical morphological traits at the species level?

I want to run a cluster analysis employing categorical morphological traits including all the described species of a genus of plants. My matrix includes both multi-state and unknown values for...

30 July 2018 3,968 6 View

Molecular Phylogeny vs DNA barcoding?

can anyone tell me the difference between simple phylogenetic studies using mitochondrial genes, and DNA barcoding, please?

07 July 2018 3,560 1 View

Are there any good tutorials or literature dealing with cluster analyses of categorical morphological traits at the species level?

I want to run a cluster analysis employing categorical morphological traits including all the described species of a genus of plants. My matrix includes both multi-state and unknown values for...

07 July 2018 6,580 9 View

Does evolution of one protein impact on the evolution of second protein or vice-versa?

I want to study the evolutionary impact of two proteins on each other from a single species, can it is possible to study through phylogenetic or computational methods and what tests and parameters...

07 July 2018 8,651 2 View

What is the best method for describing Phylogenetic relationships?

Phylogenetic relationships

07 July 2018 6,302 0 View

Calculating Functional Diversity (FD) as in Petchey & Gaston, 2002 in R?

My workspace objects: http://www.filedropper.com/workspace1_1 Hello everyone. I need help calculating FD as stated in Petchey & Gaston 2002 in R. I have a series of communities with present/absent...

07 July 2018 8,681 5 View

Can anyone tell me which R package can be used to compute phylogenetic eigenvectors?

Hello, everyone! In order to describe the phylogenetic relationships among species, I want to calculate phylogenetic eigenvectors (Diniz-Filho, Sant’Ana, & Bini,1998 ). But I do not know...

07 July 2018 4,217 3 View

Is GBS sequencing for phylogenetics effective on herbarium specimens?

There seems to be a requirement for high quality DNA. But if run with herbarium specimens maybe sequence capture and assembly are poorer relatively but adequate for phylogenetics with a reduced...

07 July 2018 1,689 3 View

Is GBS sequencing for phylogenetics effective on herbarium specimens?

There seems to be a requirement for high quality DNA. But if run with herbarium specimens maybe sequence capture and assembly are poorer relatively but adequate for phylogenetics with a reduced...

01 July 2018 7,545 3 View

What is the best method for describing Phylogenetic relationships?

Phylogenetic relationships

06 June 2018 10,082 0 View

What the heck do they mean when they write "the post-genomic era"?

What do they mean? For example here: 1. Thompson CC, Amaral GR, Campeão M, Edwards RA, Polz MF, Dutilh BE, et al. Microbial taxonomy in the post-genomic era: Rebuilding from scratch? Archives of...

06 June 2018 8,772 0 View

How could I calculate traits value considering phylogeny?

I want to calculate traits values of every plant speices considering phylogeny, e.g. traits values after removing the phylogenetic signal. I have calculate node traits values with PIC in R....

06 June 2018 1,526 0 View

Any correlation between plastome characteristics and species phylogenetic relationship?

if there is correlation, what comparative analyses can be done to support the relationship.

05 May 2018 9,117 0 View

High throughout microbial sequencing approaches; pyrosequencing, illumina can ensure the effectiveness of collected soil samples ?

By using these methods, DNA extraction, PCR amplification and bioinformatics assay are core steps to process the sequence analysis. After process the data, we have a abundant information regarding...

23 April 2018 6,439 7 View

Cytogenetics of insects, cell options for phylogenetic study?

Hi, I am interested in cytogenetics of vectors, but the group of insects that myself study, the cytogenetic analysis is only by means of male sexual cells (spermatogenesis). My question is...

04 April 2018 3,188 0 View

Under which conditions of temperature, pressure and ionic strength is ITS1 and ITS2 RNA secondary structure de novo folding most correct?

Different services are widely used for the modelling of secondary structure of internal transcribed spacers, ITS1 and ITS2, fragments of eucaryotic nuclear ribosomal gene cluster. Results of these...

04 April 2018 8,460 1 View

Is JML software is best for testing hybridization and incomplete linage sorting?

Does anyone have an experience with JML software (http://www.plantevolution.org/en/softwares.html)? My phylogenetic data have mito-nuclear discordance and I need to test whether it is...

04 April 2018 2,940 4 View

How to choose an Outgroup?

I am working on the phylogenetic relationship of two families of termites. Can I choose any other termite family as an outgroup?

04 April 2018 1,905 4 View

Is it possible to plot a circular tree with pie diagrams at nodes in Mesquite?

I've been able to plot a ball and stick tree with pie diagrams at nodes, or a circular tree without them. I want to plot a circular tree, with pie diagrams at nodes. Does anyone know of a way to...

20 March 2018 8,492 2 View

One reviewer suggested that I remove the burnin from my Bayesian phylogenetic analysis. Is this a justifiable request and why?

I have done phylogenetic analyses for both individual nuclear and mitochondrial markers- I ran the analyses with the correct model of substitution for each marker, appropriate outgroup and my...

07 March 2018 4,988 4 View

Is it possible to plot a circular tree with pie diagrams at nodes in Mesquite?

I've been able to plot a ball and stick tree with pie diagrams at nodes, or a circular tree without them. I want to plot a circular tree, with pie diagrams at nodes. Does anyone know of a way to...

03 March 2018 7,375 3 View

Applying the Bootstrap in Phylogeny Reconstruction ?

Hi dear colleagues. I want to apply bootstrap and improving the phylogenetic trees in my study. phylogenetic comparison was done by distance matrix/UPGMA analysis using Kimura 2- parameter by...

03 March 2018 10,016 4 View

BlackBox RAxML- what tree search (branch swap) method is used?

Hi there, I am using the online rapid bootstrap RAxML to run ml for my data. I cannot find out what branch swap method (i.e. NNI, SPR or TBR) RAxML uses. The manual is confusing/unclear and I...

03 March 2018 6,938 0 View

How to use DNeasy with snake scales?

I am working with a professor on a project to identify the phylogenetic affinity of rat snakes in the area, and we have been told that the DNeasy kit is good way to extract DNA. The samples we...

03 March 2018 5,176 2 View

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