Is there any user-friendly, publicly available resource to generate a phylogenetic tree from an ANI distance matrix?

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

16 June 2021 0 0 View

fatal error

16 June 2021 0 0 View

fatal error

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

Thierry De Meeûs

Hi Ralf

I do not know what is ANI but MEGA can buid a tree from any ditance matrix

Cheers

Thierry

Ralf Koebnik

Thanks a lot, Thierry,

I will look into this. ANI = Average Nucleotide Identity (at a genome-wide scale).

Best, Ralf

Vasvi Chaudhry

Dear Dr. Ralf,

You can use GENE-E (https://software.broadinstitute.org/GENE-E/). Its a java based web tool.

Best,

Vasvi

Thanks a lot, Vasvi,

I will have a look after the holidays.

All the best for 2017!

Ralf

Luis M Rodríguez-R

Hello Ralf, happy 2017!

I've been working on this resource that you may find useful: http://enve-omics.ce.gatech.edu/g-matrix, as part of the enveomics collection.

It's very recent and still in beta-testing, but you're welcome to use it. It builds an ANI (or AAI) matrix from a collection of input genomes (or proteomes) and constructs a clustering from this matrix. Note that this may not be a phylogenetic tree, since no evolutionary model is assumed. However, we've seen a good correlation of these ANI trees with phylogenetic trees, and are much more tractable (computationally) than full phylogenomic reconstructions.

Best, Miguel.

http://enve-omics.ce.gatech.edu/g-matrix