Good alignment visualization software with command line interaction?

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

Toni Gabaldón Popular answer

I'll recommend Jalview or SeaView

http://www.jalview.org/

http://pbil.univ-lyon1.fr/software/seaview.html

Andrii Tarieiev

For large aligments try to use ClustalW and Clustal omega, they are more usful for large sequences. Also exist a lot of software for this for Linux/UNIX with open code. The most part of these programms realised as a terminal, like command line in Windows.

Ionas Erb

Try Jalview:

Parameswaran Saravanan

If your sequence of interest is DNA, you can try Artemis, SeqVISTA and so on...

You can even look into kalign

Check out the links, IT may be of hel.

http://www.expasy.org/tools/#align

Toni Gabaldón

Krzysztof Moszczynski

For visualizing large data sets I'd recommend to chceck http://circos.ca/ (perfeclty worked for me with blast packages).

Wagner Arbex

You could try Consed. I think it can do what do you need.

http://www.phrap.org/consed/consed.html

http://www.ncbi.nlm.nih.gov/m/pubmed/9521923/

Balaji Rajashekar

for command line you can try

Belvu : http://seqanswers.com/wiki/Belvu (command line and GUI)

you can also try the GUI which is quite good

bioedit : http://www.mbio.ncsu.edu/bioedit/bioedit.html (only for WIndows, GUI)

Alistair C Darby

For unix I use

muscle http://www.drive5.com/muscle/

but mummer http://mummer.sourceforge.net/manual/ is good for looking at pairwise alignments and visualise larger regions.

trimAl (http://trimal.cgenomics.org) has the option -html that would output alignments in .html format, besides you can select sets of sequences or columns from your alignment if you want to focus in a region. So in a command line you could pipe your alignment program with trimal -html output and your favourite browser and have an overview on hit with the desired zoom.