Why General Time Reversible (GTR) model (Nei & Kumar 2000)?

Maximum-likelihood (ML) tree based on GTR, why we choose this GTR mode to construct a phylogenetic tree? Could anybody explain it with ref/article if there is any? I may find answer in Nei and...

03 April 2016 8,182 10 View

PCR amplification

Hi, Could you please clarify this query: if 426bp amplified for mtDNA D-loop (control region) and after editing/trimming primers finally get about 419 or 400bp. So is it correct if proceed final...

09 October 2014 7,884 4 View

How can one trim primer sequences?

Hi, is there any software to trim off primer sequence from sequence (full length sequence). Is it possible to do so using BioEdit? or is there any software to find/place primer sequence and trim...

09 October 2014 4,657 3 View

How and in which stage during initial editing/trimming or after alignment do you trim the primers off from the sequence (full length)?

08 September 2014 2,374 10 View

Does anyone have experience with Sequence alignment?

08 September 2014 5,485 13 View

Can anyone help with a problem in Arlequin performing?

I have been trying many times to perform Arlequin but following error message showing.. #[ERROR # 5] : haplotype already defined #[ERROR # 6] : unable to read sample data So where might be...

03 April 2014 5,770 6 View

How can you estimate the Nemf value and/or gene flow value (Nm)?

Is there any calculation to estimate the expected number of migrant females between/among populations per generations (Nemf), or can this be estimated by software? I can estimate pairwise Fst...

02 March 2014 657 9 View

Can anyone suggest how to prepare file for Arlequin for AMOVA?

I was trying to see the population structure of my study species. I collected samples from one study area (Sea) from one place. I did sampling from a total of 4 study areas (Seas) from each sea...

02 March 2014 4,207 7 View

Other than Arlequin, is there any software or online server recommended to do AMOVA analysis?

.

01 February 2014 7,216 6 View

DNA sequence phylogenetic tree?

I would like to take a DNA sequence from NCBI database with my samples' sequence as an outgroup to make a phylogenetic tree. so in this case, do I need to do alignment and eliminate that sequence...

01 February 2014 8,191 20 View

error in running a model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

error in modelling model in Abaqus

Excessive rotation of nodes in node set ErrNodeExcessRotation-Step1

17 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MD MOE RMSD

How to calculate the RMSD values for a MD simulation using MOE?

07 August 2021 0 0 View

MGL tools

20 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

fatal error

When I tried to energy minimization my system, I got fatal error as below. Fatal error: Atomtype opls_116 not found Although I've already added this line: ; include water #include "oplsaa.ff/spc.itp" to [molecultype] directive in my topology.

16 June 2021 0 0 View

i have some problem with chtMultiRegionSimpleFoam

--> FOAM FATAL ERROR: Maximum number of iterations exceeded From function Foam::scalar Foam::species::thermo::T(Foam::scalar, Foam::scalar, Foam::scalar, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar, Foam::scalar) const, Foam::scalar (Foam::species::thermo::*)(Foam::scalar) const) const [with Thermo = Foam::hConstThermo >; Type = Foam::sensibleEnthalpy; Foam::scalar = double; Foam::species::thermo = Foam::species::thermo >, Foam::sensibleEnthalpy>] in file /home/ubuntu/OpenFOAM/OpenFOAM-4.1/src/thermophysicalModels/specie/lnInclude/thermoI.H at line 66. FOAM aborting #0 Foam::error::printStack(Foam::Ostream&) at ??:? #1 Foam::error::abort() at ??:? #2 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::calculate() at ??:? #3 Foam::heRhoThermo >, Foam::sensibleEnthalpy> > > >::correct() at ??:? #4 ? at ??:? #5 __libc_start_main in "/lib/x86_64-linux-gnu/libc.so.6" #6 ? at ??:?

24 March 2021 0 0 View