How to add an outgroup while using supermatrix approach for species tree reconstruction?

I have 12 species from same genus. For supermatrix approach we generally use the multiple sequence alignment single copy orthologs sequences then concatenate them and remove the badly aligned...

11 December 2017 3,727 4 View

What is the difference between analysis of recombination and selection pressure when using multiple Genus vs multiple species?

I read several papers where researchers use several strains of same species for analysis of recombination or selection pressure however there are few papers in which researchers use the multiple...

09 October 2017 8,698 4 View

Do I need to stick with single copy orthologs, while estimating selection pressure with PAML?

05 June 2017 6,573 1 View

How can I evaluate the accuracy of predicted protein protein interactions with ROCR package?

02 March 2017 9,411 1 View

Which type of Tree is needed for codeml PAML analysis?

I need to run codeml for ortholog clusters from different related genus. Do I need to generate a species tree for it that I can use for all the clusters or I need to generate gene tree for all the...

01 February 2017 2,132 3 View

How to identify irreversible reactions and inconsistency of KEGG reactions?

06 July 2016 4,667 3 View

Which journals you regularly follow to increase your knowledge-base?

04 May 2016 7,465 2 View

How the large scale signaling network can be converted into Boolean model?

PS: I have single time point gene expression data for around half of the gene in the signaling network.

04 May 2016 2,919 2 View

What is the biological significance of under-representation of differentially expressed genes?

03 April 2016 3,185 5 View

How can I apply z-test for significance changes in the protein-protein interaction network properties while comparing with random networks?

03 April 2016 9,952 4 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