muscle-package: Multiple Sequence Alignment

Description Details Author(s) References See Also Examples

Description

MUSCLE performs multiple sequence alignments of nucleotide and amino acid sequences.

Details

Details about the algorithm can be found on the MUSCLE website:
http://www.drive5.com/muscle/

Author(s)

Algorithm: Robert C. Edgar

R port: Alex T. Kalinka alex.t.kalinka@gmail.com

References

Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32, 1792-1797.

See Also

muscle, umax

Examples

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5
## Align sequences in an XStringSet object.
## Not run: 
aln <- muscle(stringset = umax)

## End(Not run)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit


*** WARNING *** *Warning* Cannot open /proc/meminfo errno=13 Permission denied

MUSCLE v3.8.31 by Robert C. Edgar

http://www.drive5.com/muscle
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.

file708a46eefa78 31 seqs, max length 489, avg  length 471
00:00:00                Iter   1    0.20%  K-mer dist pass 1
00:00:00                Iter   1  100.00%  K-mer dist pass 1
00:00:00                Iter   1    0.20%  K-mer dist pass 2
00:00:00                Iter   1  100.00%  K-mer dist pass 2
00:00:00                Iter   1    3.33%  Align node       
00:00:00                Iter   1    6.67%  Align node
00:00:00                Iter   1   10.00%  Align node
00:00:00                Iter   1   13.33%  Align node
00:00:00                Iter   1   16.67%  Align node
00:00:00                Iter   1   20.00%  Align node
00:00:00                Iter   1   23.33%  Align node
00:00:00                Iter   1   26.67%  Align node
00:00:00                Iter   1   30.00%  Align node
00:00:00                Iter   1   33.33%  Align node
00:00:00                Iter   1   36.67%  Align node
00:00:00                Iter   1   40.00%  Align node
00:00:00                Iter   1   43.33%  Align node
00:00:00                Iter   1   46.67%  Align node
00:00:00                Iter   1   50.00%  Align node
00:00:00                Iter   1   53.33%  Align node
00:00:00                Iter   1   56.67%  Align node
00:00:00                Iter   1   60.00%  Align node
00:00:00                Iter   1   63.33%  Align node
00:00:00                Iter   1   66.67%  Align node
00:00:00                Iter   1   70.00%  Align node
00:00:00                Iter   1   73.33%  Align node
00:00:00                Iter   1   76.67%  Align node
00:00:00                Iter   1   80.00%  Align node
00:00:00                Iter   1   83.33%  Align node
00:00:00                Iter   1   86.67%  Align node
00:00:00                Iter   1   90.00%  Align node
00:00:00                Iter   1   93.33%  Align node
00:00:00                Iter   1   96.67%  Align node
00:00:00                Iter   1  100.00%  Align node
00:00:00                Iter   1  100.00%  Align node
00:00:00                Iter   1    3.23%  Root alignment
00:00:00                Iter   1    6.45%  Root alignment
00:00:00                Iter   1    9.68%  Root alignment
00:00:00                Iter   1   12.90%  Root alignment
00:00:00                Iter   1   16.13%  Root alignment
00:00:00                Iter   1   19.35%  Root alignment
00:00:00                Iter   1   22.58%  Root alignment
00:00:00                Iter   1   25.81%  Root alignment
00:00:00                Iter   1   29.03%  Root alignment
00:00:00                Iter   1   32.26%  Root alignment
00:00:00                Iter   1   35.48%  Root alignment
00:00:00                Iter   1   38.71%  Root alignment
00:00:00                Iter   1   41.94%  Root alignment
00:00:00                Iter   1   45.16%  Root alignment
00:00:00                Iter   1   48.39%  Root alignment
00:00:00                Iter   1   51.61%  Root alignment
00:00:00                Iter   1   54.84%  Root alignment
00:00:00                Iter   1   58.06%  Root alignment
00:00:00                Iter   1   61.29%  Root alignment
00:00:00                Iter   1   64.52%  Root alignment
00:00:00                Iter   1   67.74%  Root alignment
00:00:00                Iter   1   70.97%  Root alignment
00:00:00                Iter   1   74.19%  Root alignment
00:00:00                Iter   1   77.42%  Root alignment
00:00:00                Iter   1   80.65%  Root alignment
00:00:00                Iter   1   83.87%  Root alignment
00:00:00                Iter   1   87.10%  Root alignment
00:00:00                Iter   1   90.32%  Root alignment
00:00:00                Iter   1   93.55%  Root alignment
00:00:00                Iter   1   96.77%  Root alignment
00:00:00                Iter   1  100.00%  Root alignment
00:00:00                Iter   1  100.00%  Root alignment
00:00:00                Iter   2    3.45%  Refine tree   
00:00:00                Iter   2    6.90%  Refine tree
00:00:00                Iter   2   10.34%  Refine tree
00:00:00                Iter   2   13.79%  Refine tree
00:00:00                Iter   2   17.24%  Refine tree
00:00:00                Iter   2   20.69%  Refine tree
00:00:00                Iter   2   24.14%  Refine tree
00:00:00                Iter   2   27.59%  Refine tree
00:00:00                Iter   2   31.03%  Refine tree
00:00:00                Iter   2   34.48%  Refine tree
00:00:00                Iter   2   37.93%  Refine tree
00:00:00                Iter   2   41.38%  Refine tree
00:00:00                Iter   2   44.83%  Refine tree
00:00:00                Iter   2   48.28%  Refine tree
00:00:00                Iter   2   51.72%  Refine tree
00:00:00                Iter   2   55.17%  Refine tree
00:00:00                Iter   2   58.62%  Refine tree
00:00:00                Iter   2   62.07%  Refine tree
00:00:00                Iter   2   65.52%  Refine tree
00:00:00                Iter   2   68.97%  Refine tree
00:00:00                Iter   2   72.41%  Refine tree
00:00:00                Iter   2   75.86%  Refine tree
00:00:00                Iter   2   79.31%  Refine tree
00:00:00                Iter   2   82.76%  Refine tree
00:00:00                Iter   2   86.21%  Refine tree
00:00:00                Iter   2   89.66%  Refine tree
00:00:00                Iter   2  100.00%  Refine tree
00:00:00                Iter   2    3.23%  Root alignment
00:00:00                Iter   2    6.45%  Root alignment
00:00:00                Iter   2    9.68%  Root alignment
00:00:00                Iter   2   12.90%  Root alignment
00:00:00                Iter   2   16.13%  Root alignment
00:00:00                Iter   2   19.35%  Root alignment
00:00:00                Iter   2   22.58%  Root alignment
00:00:00                Iter   2   25.81%  Root alignment
00:00:00                Iter   2   29.03%  Root alignment
00:00:00                Iter   2   32.26%  Root alignment
00:00:00                Iter   2   35.48%  Root alignment
00:00:00                Iter   2   38.71%  Root alignment
00:00:00                Iter   2   41.94%  Root alignment
00:00:00                Iter   2   45.16%  Root alignment
00:00:00                Iter   2   48.39%  Root alignment
00:00:00                Iter   2   51.61%  Root alignment
00:00:00                Iter   2   54.84%  Root alignment
00:00:00                Iter   2   58.06%  Root alignment
00:00:00                Iter   2   61.29%  Root alignment
00:00:00                Iter   2   64.52%  Root alignment
00:00:00                Iter   2   67.74%  Root alignment
00:00:00                Iter   2   70.97%  Root alignment
00:00:00                Iter   2   74.19%  Root alignment
00:00:00                Iter   2   77.42%  Root alignment
00:00:00                Iter   2   80.65%  Root alignment
00:00:00                Iter   2   83.87%  Root alignment
00:00:00                Iter   2   87.10%  Root alignment
00:00:00                Iter   2   90.32%  Root alignment
00:00:00                Iter   2   93.55%  Root alignment
00:00:00                Iter   2   96.77%  Root alignment
00:00:00                Iter   2  100.00%  Root alignment
00:00:00                Iter   2  100.00%  Root alignment
00:00:00                Iter   2  100.00%  Root alignment
00:00:00                Iter   3    3.39%  Refine biparts
00:00:00                Iter   3    5.08%  Refine biparts
00:00:00                Iter   3    6.78%  Refine biparts
00:00:00                Iter   3    8.47%  Refine biparts
00:00:00                Iter   3   10.17%  Refine biparts
00:00:00                Iter   3   11.86%  Refine biparts
00:00:00                Iter   3   13.56%  Refine biparts
00:00:00                Iter   3   15.25%  Refine biparts
00:00:00                Iter   3   16.95%  Refine biparts
00:00:00                Iter   3   18.64%  Refine biparts
00:00:00                Iter   3   20.34%  Refine biparts
00:00:00                Iter   3   22.03%  Refine biparts
00:00:00                Iter   3   23.73%  Refine biparts
00:00:00                Iter   3   25.42%  Refine biparts
00:00:00                Iter   3   27.12%  Refine biparts
00:00:00                Iter   3   28.81%  Refine biparts
00:00:00                Iter   3   30.51%  Refine biparts
00:00:00                Iter   3   32.20%  Refine biparts
00:00:00                Iter   3   33.90%  Refine biparts
00:00:00                Iter   3   35.59%  Refine biparts
00:00:00                Iter   3   37.29%  Refine biparts
00:00:00                Iter   3   38.98%  Refine biparts
00:00:00                Iter   3   40.68%  Refine biparts
00:00:00                Iter   3   42.37%  Refine biparts
00:00:00                Iter   3   44.07%  Refine biparts
00:00:00                Iter   3   45.76%  Refine biparts
00:00:00                Iter   3   47.46%  Refine biparts
00:00:00                Iter   3   49.15%  Refine biparts
00:00:00                Iter   3   50.85%  Refine biparts
00:00:00                Iter   3   52.54%  Refine biparts
00:00:00                Iter   3   54.24%  Refine biparts
00:00:00                Iter   3   55.93%  Refine biparts
00:00:00                Iter   3   57.63%  Refine biparts
00:00:00                Iter   3   59.32%  Refine biparts
00:00:00                Iter   3   61.02%  Refine biparts
00:00:00                Iter   3   62.71%  Refine biparts
00:00:00                Iter   3   64.41%  Refine biparts
00:00:00                Iter   3   66.10%  Refine biparts
00:00:00                Iter   3   67.80%  Refine biparts
00:00:00                Iter   3   69.49%  Refine biparts
00:00:00                Iter   3   71.19%  Refine biparts
00:00:00                Iter   3   72.88%  Refine biparts
00:00:00                Iter   3   74.58%  Refine biparts
00:00:00                Iter   3   76.27%  Refine biparts
00:00:01                Iter   3   77.97%  Refine biparts
00:00:01                Iter   3   79.66%  Refine biparts
00:00:01                Iter   3   81.36%  Refine biparts
00:00:01                Iter   3   83.05%  Refine biparts
00:00:01                Iter   3   84.75%  Refine biparts
00:00:01                Iter   3   86.44%  Refine biparts
00:00:01                Iter   3   88.14%  Refine biparts
00:00:01                Iter   3   89.83%  Refine biparts
00:00:01                Iter   3   91.53%  Refine biparts
00:00:01                Iter   3   93.22%  Refine biparts
00:00:01                Iter   3   94.92%  Refine biparts
00:00:01                Iter   3   96.61%  Refine biparts
00:00:01                Iter   3   98.31%  Refine biparts
00:00:01                Iter   3  100.00%  Refine biparts
00:00:01                Iter   3  101.69%  Refine biparts
00:00:01                Iter   3  100.00%  Refine biparts
00:00:01                Iter   4    3.39%  Refine biparts
00:00:01                Iter   4    5.08%  Refine biparts
00:00:01                Iter   4    6.78%  Refine biparts
00:00:01                Iter   4    8.47%  Refine biparts
00:00:01                Iter   4   10.17%  Refine biparts
00:00:01                Iter   4   11.86%  Refine biparts
00:00:01                Iter   4   13.56%  Refine biparts
00:00:01                Iter   4   15.25%  Refine biparts
00:00:01                Iter   4   16.95%  Refine biparts
00:00:01                Iter   4   18.64%  Refine biparts
00:00:01                Iter   4   20.34%  Refine biparts
00:00:01                Iter   4   22.03%  Refine biparts
00:00:01                Iter   4   23.73%  Refine biparts
00:00:01                Iter   4   25.42%  Refine biparts
00:00:01                Iter   4   27.12%  Refine biparts
00:00:01                Iter   4   28.81%  Refine biparts
00:00:01                Iter   4   30.51%  Refine biparts
00:00:01                Iter   4   32.20%  Refine biparts
00:00:01                Iter   4   33.90%  Refine biparts
00:00:01                Iter   4   35.59%  Refine biparts
00:00:01                Iter   4   37.29%  Refine biparts
00:00:01                Iter   4   38.98%  Refine biparts
00:00:01                Iter   4   40.68%  Refine biparts
00:00:01                Iter   4   42.37%  Refine biparts
00:00:01                Iter   4   44.07%  Refine biparts
00:00:01                Iter   4   45.76%  Refine biparts
00:00:01                Iter   4   47.46%  Refine biparts
00:00:01                Iter   4   49.15%  Refine biparts
00:00:01                Iter   4   50.85%  Refine biparts
00:00:01                Iter   4   52.54%  Refine biparts
00:00:01                Iter   4   54.24%  Refine biparts
00:00:01                Iter   4   55.93%  Refine biparts
00:00:01                Iter   4   57.63%  Refine biparts
00:00:01                Iter   4   59.32%  Refine biparts
00:00:01                Iter   4   61.02%  Refine biparts
00:00:01                Iter   4   62.71%  Refine biparts
00:00:01                Iter   4   64.41%  Refine biparts
00:00:01                Iter   4   66.10%  Refine biparts
00:00:01                Iter   4   67.80%  Refine biparts
00:00:01                Iter   4   69.49%  Refine biparts
00:00:01                Iter   4   71.19%  Refine biparts
00:00:01                Iter   4   72.88%  Refine biparts
00:00:01                Iter   4   74.58%  Refine biparts
00:00:01                Iter   4   76.27%  Refine biparts
00:00:01                Iter   4   77.97%  Refine biparts
00:00:01                Iter   4   79.66%  Refine biparts
00:00:01                Iter   4   81.36%  Refine biparts
00:00:01                Iter   4   83.05%  Refine biparts
00:00:01                Iter   4   84.75%  Refine biparts
00:00:01                Iter   4   86.44%  Refine biparts
00:00:01                Iter   4   88.14%  Refine biparts
00:00:01                Iter   4   89.83%  Refine biparts
00:00:01                Iter   4   91.53%  Refine biparts
00:00:01                Iter   4   93.22%  Refine biparts
00:00:01                Iter   4   94.92%  Refine biparts
00:00:01                Iter   4   96.61%  Refine biparts
00:00:01                Iter   4   98.31%  Refine biparts
00:00:01                Iter   4  100.00%  Refine biparts
00:00:01                Iter   4  101.69%  Refine biparts
00:00:01                Iter   4  100.00%  Refine biparts

muscle documentation built on Nov. 8, 2020, 8:12 p.m.