Dear Vijesh Kumar,

try Mega (Molecular evolutionary genetics analysis) tool. It allows to choose different algorithms for MSA and phylogenetic analysis.  

Dear Vijesh Kumar,

try Mega (Molecular evolutionary genetics analysis) tool. It allows to choose different algorithms for MSA and phylogenetic analysis.  

I have had a good experience with PRANK for MSA and RAxML for drawing trees. If you want to identify unique or interesting domains (e.g. things that look like they are under selection) then codeml (in the PAML software package) is a nice analysis tool that compares synonymous and non-synonymous substitutions across multiple sequences and a phylogenetic tree.

Hi Vignesh,

For easy use, you can prefer some online tools such as Clustal Omega (http://www.ebi.ac.uk/Tools/msa/clustalo/). For advanced parameters as Aditya said, MEGA software could be a best choice. It is freely available. Drawing tress under ML method using MEGA software has shown better results. You can avail a free version of MEGA from http://www.megasoftware.net/

Thank You, Aditya, Axel and Sneha....

Hi Vijesh,

For MSA I would recommend PASTA or Prank. Prank is particularly useful if you need in-frame alignments. I would avoid global alignment programs - local alignment programs tend to be more reliable.

To build a tree I would use RAxML (maximum likelihood-based), or MrBayes or BEAST (Bayesian-based). For RAxML I typically run for 1000 bootstraps, and for Bayesian approaches I run the MCMC until stationarity and convergence are reached. 

I use Interproscan and NCBI's conserved protein domain finder to identify protein domains.

I hope this helps!

Adam

Hi Vijesh

Some references 1

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwis1Z64w6_YAhWFHJoKHS3rCcoQFggnMAA&url=http%3A%2F%2Fwww.letunic.com%2Fpublications%2F20195253.pdf&usg=AOvVaw1OyIAzrc8GaQ3jNlBLRX6D

2

https://www.biostars.org/p/77617/

3

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=4&cad=rja&uact=8&ved=0ahUKEwjGlZvWw6_YAhUkS5oKHd8PCgIQFghAMAM&url=https%3A%2F%2Fwww.tacoma.uw.edu%2Fsites%2Fdefault%2Ffiles%2Fglobal%2Fdocuments%2Finstitute_tech%2Frpotter.pdf&usg=AOvVaw329PfBSSMnBZssizCti5nq

4

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=5&cad=rja&uact=8&ved=0ahUKEwjGlZvWw6_YAhUkS5oKHd8PCgIQFghIMAQ&url=https%3A%2F%2Fcommunity.gep.wustl.edu%2Frepository%2Fcourse_materials_GEP_partners%2FSusan_Parrish_MSA_Clustal_Omega.pdf&usg=AOvVaw1U58iwUgqS88_IVzx7noAv

5

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=6&cad=rja&uact=8&ved=0ahUKEwjGlZvWw6_YAhUkS5oKHd8PCgIQFghOMAU&url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fbooks%2FNBK21122%2F&usg=AOvVaw21XYYxQfp7Mb1C-gwBKqch

6

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=7&cad=rja&uact=8&ved=0ahUKEwjGlZvWw6_YAhUkS5oKHd8PCgIQFghXMAY&url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC4894340%2F&usg=AOvVaw1U5xIYmCAJL1hBvyLFcNTR

7

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=8&cad=rja&uact=8&ved=0ahUKEwjGlZvWw6_YAhUkS5oKHd8PCgIQFghfMAc&url=https%3A%2F%2Facademic.oup.com%2Fmbe%2Farticle%2F30%2F5%2F1229%2F992850&usg=AOvVaw0hDTtogtIhPRokoJXOp7S3

8

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=9&cad=rja&uact=8&ved=0ahUKEwjGlZvWw6_YAhUkS5oKHd8PCgIQFghlMAg&url=http%3A%2F%2Ftandy.cs.illinois.edu%2Fwarnow-mage-paper.pdf&usg=AOvVaw1sjjJSognl2aVYOGv0-MUa

9

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=10&cad=rja&uact=8&ved=0ahUKEwjGlZvWw6_YAhUkS5oKHd8PCgIQFghuMAk&url=https%3A%2F%2Fwww.omicsonline.org%2Fopen-access%2Fmolecular-markers-in-phylogenetic-studiesa-review-2329-9002-2-131.php%3Faid%3D30965&usg=AOvVaw0_4fQA1K26mos45uAbMiSX

10

https://bitesizebio.com/33080/phylogenetic-tree-construction-easy-blast-mega/

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=12&cad=rja&uact=8&ved=0ahUKEwixwJP9xK_YAhWFFZoKHS_wBsI4ChAWCDYwAQ&url=http%3A%2F%2Fetetoolkit.org%2Fdocs%2F2.3%2Ftutorial%2Ftutorial_phylogeny.html&usg=AOvVaw0ZlEo8rI6-lBu6aPQiZ9u0

12

https://books.google.iq/books?id=-FSGAgAAQBAJ&pg=PA280&lpg=PA280&dq=multiple+sequence+alignment+for+a+particular+gene,+drawing+the+phylogenetic+tree&source=bl&ots=mlzRaeqdTs&sig=yRrKWIK8kKid-pMKbMIirduJ0kc&hl=en&sa=X&ved=0ahUKEwixwJP9xK_YAhWFFZoKHS_wBsI4ChDoAQhUMAY

13

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=18&cad=rja&uact=8&ved=0ahUKEwixwJP9xK_YAhWFFZoKHS_wBsI4ChAWCFgwBw&url=http%3A%2F%2Fwww.virology.wisc.edu%2Facp%2FTutorials%2FMEGA.pdf&usg=AOvVaw1O8wQOxEC7rSjpXKDhAC5R

14

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=19&cad=rja&uact=8&ved=0ahUKEwixwJP9xK_YAhWFFZoKHS_wBsI4ChAWCF0wCA&url=https%3A%2F%2Fwww.expasy.org%2Fgenomics%2Fsequence_alignment&usg=AOvVaw0HMNJaY-3o3cxQiELeAYTL

15

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=20&cad=rja&uact=8&ved=0ahUKEwixwJP9xK_YAhWFFZoKHS_wBsI4ChAWCGMwCQ&url=https%3A%2F%2Fwww.patricbrc.org%2Fcontent%2FMultiple_Sequence_Alignment&usg=AOvVaw31K6pxElRoVRcXD2MW6AGZ

16

http://www.evolution-textbook.org/content/free/contents/ch27.html

17

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=22&cad=rja&uact=8&ved=0ahUKEwjosMT9zq_YAhUnP5oKHf7TCKk4FBAWCDkwAQ&url=http%3A%2F%2Fgenome.cshlp.org%2Fcontent%2F17%2F2%2F127.full&usg=AOvVaw2eHL7MLXPmXXN05hQ8Qp-Q

18

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=23&cad=rja&uact=8&ved=0ahUKEwjosMT9zq_YAhUnP5oKHf7TCKk4FBAWCEEwAg&url=http%3A%2F%2Fbioinformatics.org%2Fsoftware%2Fmol_linux.php3&usg=AOvVaw05jZVU2UGOBI0LYYegEXKs

19

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=24&cad=rja&uact=8&ved=0ahUKEwjosMT9zq_YAhUnP5oKHf7TCKk4FBAWCEcwAw&url=http%3A%2F%2Fjournals.plos.org%2Fplosbiology%2Farticle%3Fid%3D10.1371%2Fjournal.pbio.1000602&usg=AOvVaw3pmXX_xD_sSIqsXHdF9CrU

20

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=25&cad=rja&uact=8&ved=0ahUKEwjosMT9zq_YAhUnP5oKHf7TCKk4FBAWCFEwBA&url=https%3A%2F%2Fwww.sciencedirect.com%2Ftopics%2Fmedicine-and-dentistry%2Fmultiple-sequence-alignment&usg=AOvVaw0F59r4A3BIc67CM7in3o2C