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OMM_MACSE

Align coding sequences using MACSE (OrthoMaM pipeline).



proposed by : Vincent RANWEZ

MACSE

MACSE web site

OrthoMaM_v10b

Required field icon required conditionally required optional
E-mail

All options

> Sequences
> Less reliable sequences


Enter coding sequences to align and filter (FASTA format):
  1. Select a file:
  2. or paste your data here:




Enter less reliable coding sequences to align and filter (FASTA format):
  1. Select a file:
  2. or paste your data here:

Select genetic code

Use Macse to detect frameshifts ?

Prefilter non homologous fragments ?

Filter isolated amino acids ?

Replace frameshifts by standart chararcter ?


E-mail

References:
If you use this pipeline in your work please cite:

+ MACSE
Ranwez V., Harispe S., Delsuc F., Douzery E.J.P. (2011). MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PloS one, 6(9), e22594.

+ MAFFT or MUSCLE
Katoh K., Standley D.M. (2013). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular biology and evolution, 30(4), 772-780. Edgar R.C. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research, 32(5), 1792-1797.

+ HMMCleaner
Philippe H., de Vienne D.M., Ranwez V., Roure B., Baurain D., Delsuc F. (2017). Pitfalls in supermatrix phylogenomics. European Journal of Taxonomy, 283, 1-25.

+ OrthoMaM
Douzery E.J.P., Scornavacca C., Romiguier J., Belkhir K., Galtier N., Delsuc F., Ranwez V. (2014). OrthoMaM v8: a database of orthologous exons and coding sequences for comparative genomics in mammals. Molecular biology and evolution, 31(7), 1923-1928.



Based on Pise form generator version: 5.a (23 janv. 2018 11:09)