In drostlab/orthologr: Comparative Genomics with R
The orthologr package provides multiple functions to perform pairwise and multiple sequence alignments. The following functions are implemented in orthologr:
multi_aln() : Perform Multiple Sequence Alignmentspairwise_aln() : Perform Pairwise Sequence Alignmentscodon_aln() : Perform Codon Alignments
Getting Started
Prior to be able to use all sequence alignment functions implemented in orthologr
you need to install corresponding alignment tools of interest.
The above mentioned functions provide interfaces to the following alignment programs:
The multi_aln() function
-
ClustalW : Advanced multiple alignment tool of nucleic acid and protein sequences
-
T_Coffee : A collection of tools for processing multiple sequence alignments
of nucleic acids and proteins as well as their 3D structure
-
MUSCLE : Fast and accurate multiple alignment tool of nucleic acid and protein sequences
-
ClustalO : Fast and scalable multiple alignment tool for nucleic acid and protein sequences that is also
capable of performing HMM alignments
-
MAFFT : A tool for multiple sequence alignment and phylogeny
The easiest way to use the multi_aln() function is to store the corresponding multiple sequence alignment tools in the default execution PATH of you system (e.g. /usr/local/bin on UNIX machines).
You can test whether the corresponding multiple sequence alignment tool can be executed from the default PATH by running:
ClustalW
-
MacOS: system("clustalw2 -help")
-
Linux: system("clustalw -help")
-
Windows: system("clustalw2.exe -help")
In case everything is installed appropriately, you should see:
CLUSTAL 2.1 Multiple Sequence Alignments
DATA (sequences)
-INFILE=file.ext :input sequences.
-PROFILE1=file.ext and -PROFILE2=file.ext :profiles (old alignment).
VERBS (do things)
-OPTIONS :list the command line parameters
-HELP or -CHECK :outline the command line params.
-FULLHELP :output full help content.
-ALIGN :do full multiple alignment.
Perform A Multiple Alignment Using ClustalW
The multi_aln() function takes a fasta file storing the genes (proteins) that shall
be aligned. The tool argument specifies the alignment tool that shall be used to perform
a multiple sequence alignment (in this case tool = clustalw). The get_aln argument specifies whether or not the alignment shall be printed out to the console. In case get_aln = FALSE, the corresponding alignment
file is stored in the file.path(tempdir(),_alignment,multi_aln) directory.
# in case the default execution path of clustalw runs properly on your system
orthologr::multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
tool = "clustalw",
get_aln = TRUE)
CLUSTAL 2.1 Multiple Sequence Alignments
[1] "Multiple Alignment successfully written in /var/folders/tb/
v6lh8_g505bfjytt3lvdmvw00000gn/T//RtmpOXdtWL/_alignment/multi_aln/clustalw.aln."
AAMultipleAlignment with 2 rows and 429 columns
aln names
[1] MEDQVGFGFRPNDEELVGHYLRNKIEGNTSRDVEVAISEVNICSYD...IKIPPSTNTVKQSWIVLENAQWNYLKNMIIGVLLFISVISWIILVG AT1G01010.1
[2] --------MAASEHRCVGCGFR---------------VKSLFIQYS...IFEP-------TIFLTQFGSLMQYLSYLFRTV-------------- 333554|PACid_1603...
It is also possible to pass additional parameters to the ClustalW call:
# running clustalw using additional parameters
# details: system("clustalw2 -help")
orthologr::multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
tool = "clustalw",
get_aln = TRUE,
params = "-PWMATRIX=BLOSUM -TYPE=PROTEIN")
CLUSTAL 2.1 Multiple Sequence Alignments
Sequence type explicitly set to Protein
Sequence format is Pearson
Sequence 1: AT1G01010.1 429 aa
Sequence 2: 333554|PACid_16033839 245 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 2
Guide tree file created: [/Library/Frameworks/R.framework/Versions/3.1/Resources/library/orthologr/seqs/aa_seqs.dnd]
There are 1 groups
Start of Multiple Alignment
Aligning...
Group 1: Delayed
Alignment Score 29
CLUSTAL-Alignment file created [/var/folders/tb/v6lh8_g505bfjytt3lvdmvw00000gn/T//RtmpOXdtWL/_alignment/multi_aln/clustalw.aln]
[1] "Multiple Alignment successfully written in /var/folders/tb/v6lh8_g505bfjytt3lvdmvw00000gn/T//RtmpOXdtWL/_alignment/multi_aln/clustalw.aln."
AAMultipleAlignment with 2 rows and 429 columns
aln names
[1] MEDQVGFGFRPNDEELVGHYLRNKIEGNTSRDVEVAISEVNICSYD...IKIPPSTNTVKQSWIVLENAQWNYLKNMIIGVLLFISVISWIILVG AT1G01010.1
[2] --------MAASEHRCVGCGFR---------------VKSLFIQYS...IFEP-------TIFLTQFGSLMQYLSYLFRTV-------------- 333554|PACid_1603...
T_COFFEE
system("t_coffee -version")
In case everything is installed appropriately, you should see:
PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 21:55:14 - Revision 8cbe486 - Build 470)
orthologr::multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
tool = "t_coffee",
get_aln = TRUE)
MUSCLE
system("muscle -help")
In case everything is installed appropriately, you should see:
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.
Basic usage
muscle -in <inputfile> -out <outputfile>
Common options (for a complete list please see the User Guide):
-in <inputfile> Input file in FASTA format (default stdin)
-out <outputfile> Output alignment in FASTA format (default stdout)
-diags Find diagonals (faster for similar sequences)
-maxiters <n> Maximum number of iterations (integer, default 16)
-maxhours <h> Maximum time to iterate in hours (default no limit)
-html Write output in HTML format (default FASTA)
-msf Write output in GCG MSF format (default FASTA)
-clw Write output in CLUSTALW format (default FASTA)
-clwstrict As -clw, with 'CLUSTAL W (1.81)' header
-log[a] <logfile> Log to file (append if -loga, overwrite if -log)
-quiet Do not write progress messages to stderr
-version Display version information and exit
Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
Fastest possible (nucleotides): -maxiters 1 -diags
# in case the default execution path of muscle runs properly on your system
multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
tool = "muscle",
get_aln = TRUE)
ClustalO
system("clustalo --help")
# in case the default execution path of muscle runs properly on your system
multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
tool = "clustalo",
get_aln = TRUE)
MAFFT
system("mafft -help")
In case everything is installed appropriately, you should see:
------------------------------------------------------------------------------
MAFFT v7.187 (2014/10/02)
http://mafft.cbrc.jp/alignment/software/
MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
------------------------------------------------------------------------------
High speed:
% mafft in > out
% mafft --retree 1 in > out (fast)
High accuracy (for <~200 sequences x <~2,000 aa/nt):
% mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok)
% mafft --maxiterate 1000 --genafpair in > out (% einsi in > out)
% mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)
If unsure which option to use:
% mafft --auto in > out
--op # : Gap opening penalty, default: 1.53
--ep # : Offset (works like gap extension penalty), default: 0.0
--maxiterate # : Maximum number of iterative refinement, default: 0
--clustalout : Output: clustal format, default: fasta
--reorder : Outorder: aligned, default: input order
--quiet : Do not report progress
--thread # : Number of threads (if unsure, --thread -1)
The multi_aln() function
The multi_aln() function is an interface function between R and common multiple sequence alignment tools. When working with this function a new folder named _alignment is being created and stores the multiple alignment returned by the corresponding alignment tool. The argument get_aln = TRUE allows to work with the multiple alignment generated by the corresponding alignment tool within the current R session.
This small pairwise alignment example shall illustrate how the multi_aln() output can be used:
multi_aln(system.file('seqs/aa_seqs.fasta', package = 'orthologr'),
tool = "clustalw", get_aln = TRUE)
$nb
[1] 2
$nam
[1] "AT1G01010.1" "333554|PACid_16033839"
$seq
$seq[[1]]
[1] "medqvgfgfrpndeelvghylrnkiegntsrdvevaisevnicsydpwnlrfqskyksrdamwyffsrrennk
gnrqsrttvsgkwkltgesvevkdqwgfcsegfrgkighkrvlvfldgrypdktksdwvihefhydllpehqrtyvic
rleykgddadilsayaidptpafvpnmtssagsvvnqsrqrnsgsyntyseydsanhgqqfnensnimqqqplqgsfn
plleydfanhggqwlsdyidlqqqvpylapyenesemiwkhvieenfeflvdertsmqqhysdhrpkkpvsgvlpdds
sdtetgsmifedtssstdsvgssdepghtriddipslniieplhnykaqeqpkqqskekvissqksecewkmaedsik
ippstntvkqswivlenaqwnylknmiigvllfisviswiilvg"
$seq[[2]]
[1] "--------maasehrcvgcgfr---------------vkslfiqyspgnirlmk-------------------
---------------cgnckevadey----------iecermiifid---------------------lilhrpkvyr
hvlynainpetvniqhllwklvfvyllldsyrslllrrtdeess----------------fshssvlisikvligvls
anaafifs----------------------------------------faiaakgllnevs---rgreimlgicissy
fkifllamlvwefp----------------msvifivdilvltsnsmalkvmtestmtrciavcliahlvrfsvgqif
ep-------tifltqfgslmqylsylfrtv--------------"
$com
[1] NA
attr(,"class")
[1] "alignment"
Furthermore, multiple alignments are returned as follows:
multi_aln(system.file('seqs/multi_aln_example.fasta', package = 'orthologr'),
tool = "clustalw", get_aln = TRUE)
CLUSTAL 2.1 Multiple Sequence Alignments
$nb
[1] 4
$nam
[1] "AT1G01010.1|PACid_19656964" "Thhalv10006531m|PACid_20187082"
[3] "Bra032623|PACid_22715924" "311315|PACid_16059488"
$seq
$seq[[1]]
[1] "-----------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
-----------------------------------------medqvgfg------------------frp
ndeelvghylrnkiegntsr----------dvevaisevnicsydp---------wnlrfqskyksrd--
-------amwyffsrre------------nnkgnrqsrttvsgkwkltgesvevkdqwgfcseg------
--frgkig-------------------------------------------hkrvlvfldgrypdktksd
wvihefhydllpehqr-----------------tyvicr--leykgddadilsayaidptpafvpnmtss
agsvvnqsrqrnsgsyntyseydsanhgqqfnensn-imqqqplqgsfnplleydfanhg-------gqw
l----------------------------sdyidlqqqvpylapye------------------------
-----------------------------------nesemiwkhvieenfeflvdertsmqqhysdhrpk
kpvsgvlp----------------ddssdtetgsmifedtssstds------------------------
---------------------------------vgssdepghtriddipslniieplhnykaqeqpkqqs
kekvissqksecewkmaeds---------ikippstntvkqswivlenaqwnylknmiigvllfisvisw
iilvg-------------------------------"
$seq[[2]]
[1] "mvmederrgdikppsywldacediscdliddlvsdfdpssvavaesvdengvnndffggidhild
siknggglpnrahingvsetnsqringnsevseaaqliagettvsvkgnvlqkcggkrdevskeegeknr
krarvcsyqrersnlsgrgqansregdrfmnrkrtrnwdeaghnkrrdgynyrrdgrdreargywerdkv
gsnelvyrsgtweadherdlkkesgrnresdekaeenkskpeehkekvveeqarryqldvleqakaknti
afletgagktliailliksihkdltsqnrkmlsvflvpkvplvyqqaevirnqtcfqvghycgemgqdfw
darrwqrefeskqvlvmtaqillnilrhsiirmeainllildechhavkkhpyslvmsefyhttpkdkrp
aifgmtaspvnlkgvssqvdcaikirnletkldstvctikdrkelekhvpmpseivveydkaatmwslhe
kikqmiaaveeaaqassrkskwqfmgardagakdelrqvygvsertesdgaanlihklrainytlaelgq
wcaykvaqsfltalqsdervnfqvdvkfqesylsevvsllqcellegaaaekavaelskpengnandeie
egelpddhvvsggehvdkvigaavadgkvtpkvqsliklllkyqhtadfraivfvervvaalvlpkvfae
lpslgfircasmighnnsqemkssqmqdtiskfrdgqvtllvatsvaeegldirqcnvvmrfdlaktvla
yiqsrgrarkpgsdyilmverenvshaaflrnarnseetlrkeaiertdlshlkdssrlisidavpgtvy
kveatgamvslnsavglihfycsqlpgdryailrpefsmvkhekpgghteyscrlqlpcnapfeilegpv
cssmrlaqqavclagckklhemgaftdmllpdkgsgqdaekadqddegepipgtarhrefypegvadvlk
gewilsgkeicessklfhlymysvrcvdsgvskdpfltevsefavlfgneldaevlsmsmdlyvaramit
kaslafrgslditesqlssikkfhvrlmsivldvdvepsttpwdpakaylfvpvadnssaepikginwel
vekitkttvwdnplqrarpdvylgtnertlggdrreygfgklrhnigfgqkshptygirgavasfdvvra
sgllpvrdalekevegdlsqgklmmadgcmvaenllgkivtaahsgkrfyvdsicydmsaetsfprkegy
lgpleyntyadyykqkygvdlsckqqplikgrgvsycknllsprfeqsgesetildktyyvflppelcvv
hplsgslvrgaqrlpsimrrvesmllavqlknlisypiptskilealtaascqetfcyeraellgdaylk
wivsrflflkypqkhegqltrmrqqmvsnlvlyqyalvkglqsyiqadrfapsrwsapgvppvydedtkd
ggssffdeeekpegnkdvfedgemedgelegdlssyrvlssktladvvealigvyyveggktaanhlmkw
igihveddpeetegsvkpvynvpesvlksidfvgleralkyeftekgllveaithasrpssgvscyqrle
fvgdavldhlitrhlfftytslppgrltdlraaavnnenfarvavkhklhlylrhgssalekqirdfvke
vltesskpgfnsfglgdckapkvlgdivesiagaifldsgkdttaawkvfqpllqpmvtpetlpmhpvre
lqercqqqaegleykasrsgntatvevfidgvqvgaaqnpqkkmaqklaarnalaalkekeaeeskkkqa
ngnaagenqddnengnkkngnqtftrqtlndiclrknwpmpsyrcvkeggpahakrftfgvrvntsdrgw
tdecigepmpsvkkakdsaailllellnktys----"
$seq[[3]]
[1] "-----------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
-----------------------------------------------mqqppqmfpmapsmpptnitteq
iqkyleenkklimaimenqnlgklaecaqyqallqknlmylaaiadaqpppstagatppp----------
---------------------------------amasqmgaphpg-------------------------
---------------------------------------------mqppsyfmqhp------qasgmaqq
appagifp----------------------prgplqfgsphqlqdp------------------------
-----------------------------------qqqhmhqqamqghmgmrpmginnnngmqhqmqqqp
etslggsaanvgirggkqdg-------------------------adgqgkddgk---------------
------------------------------------"
$seq[[4]]
[1] "-----------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
----------------------------------------------------------------------
--------------------------------------------------------mlslnmrteienlw
vfalaskfnifmqehfaslllaiaitwctltivfwstpggpawg--------------------------
--------------------------kyfftrrfsslghnrksknlipgprgfplvgsmslrsshvahqr
iasvaemsnakrlmafslgdtkvvvtchpdvakeilnssvfadrpvdetayg---lmfnramgfapngty
wrtlrrlssnhlfnpkqikrseeqrrviatqmvnafarnaksafavrdllktaslcnmmglvfg------
-----------------------------------------------------reyelesnnnveseclk
glveegydllg-----------------------tlnwtdhlpwlagldfqqirfrcsqlvpkvnlllsr
iihehyatgnfldvllslqrseklsdsdivavlwemifrgtdtvavliewvlarialhpk----------
----------------------------------vqstvhdeldr-------------------------
---------------------------------------------vvgrsrtvdesdlpsltyltamike
vlr--lhp-----------------------pgpllswarlsitdt------------------------
------------------------------------tvdgyhvpagttamvnmwaiardphvwedplefk
perfvakdgeaefsvfgsdlr---------------lapfgsgkrvcpgknlglttvsfwvatllhefew
lpsveanppdlsevlrlscemacplivnvsprrksv"
$com
[1] NA
attr(,"class")
[1] "alignment"
drostlab/orthologr documentation built on Oct. 13, 2023, 3:26 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
The orthologr package provides multiple functions to perform pairwise and multiple sequence alignments. The following functions are implemented in orthologr:
multi_aln(): Perform Multiple Sequence Alignmentspairwise_aln(): Perform Pairwise Sequence Alignmentscodon_aln(): Perform Codon Alignments
Getting Started
Prior to be able to use all sequence alignment functions implemented in orthologr
you need to install corresponding alignment tools of interest.
The above mentioned functions provide interfaces to the following alignment programs:
The multi_aln() function
-
ClustalW : Advanced multiple alignment tool of nucleic acid and protein sequences
-
T_Coffee : A collection of tools for processing multiple sequence alignments of nucleic acids and proteins as well as their 3D structure
-
MUSCLE : Fast and accurate multiple alignment tool of nucleic acid and protein sequences
-
ClustalO : Fast and scalable multiple alignment tool for nucleic acid and protein sequences that is also capable of performing HMM alignments
-
MAFFT : A tool for multiple sequence alignment and phylogeny
The easiest way to use the multi_aln() function is to store the corresponding multiple sequence alignment tools in the default execution PATH of you system (e.g. /usr/local/bin on UNIX machines).
You can test whether the corresponding multiple sequence alignment tool can be executed from the default PATH by running:
ClustalW
-
MacOS:
system("clustalw2 -help") -
Linux:
system("clustalw -help") -
Windows:
system("clustalw2.exe -help")
In case everything is installed appropriately, you should see:
CLUSTAL 2.1 Multiple Sequence Alignments
DATA (sequences)
-INFILE=file.ext :input sequences.
-PROFILE1=file.ext and -PROFILE2=file.ext :profiles (old alignment).
VERBS (do things)
-OPTIONS :list the command line parameters
-HELP or -CHECK :outline the command line params.
-FULLHELP :output full help content.
-ALIGN :do full multiple alignment.
Perform A Multiple Alignment Using ClustalW
The multi_aln() function takes a fasta file storing the genes (proteins) that shall
be aligned. The tool argument specifies the alignment tool that shall be used to perform
a multiple sequence alignment (in this case tool = clustalw). The get_aln argument specifies whether or not the alignment shall be printed out to the console. In case get_aln = FALSE, the corresponding alignment
file is stored in the file.path(tempdir(),_alignment,multi_aln) directory.
# in case the default execution path of clustalw runs properly on your system orthologr::multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'), tool = "clustalw", get_aln = TRUE)
CLUSTAL 2.1 Multiple Sequence Alignments
[1] "Multiple Alignment successfully written in /var/folders/tb/
v6lh8_g505bfjytt3lvdmvw00000gn/T//RtmpOXdtWL/_alignment/multi_aln/clustalw.aln."
AAMultipleAlignment with 2 rows and 429 columns
aln names
[1] MEDQVGFGFRPNDEELVGHYLRNKIEGNTSRDVEVAISEVNICSYD...IKIPPSTNTVKQSWIVLENAQWNYLKNMIIGVLLFISVISWIILVG AT1G01010.1
[2] --------MAASEHRCVGCGFR---------------VKSLFIQYS...IFEP-------TIFLTQFGSLMQYLSYLFRTV-------------- 333554|PACid_1603...
It is also possible to pass additional parameters to the ClustalW call:
# running clustalw using additional parameters # details: system("clustalw2 -help") orthologr::multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'), tool = "clustalw", get_aln = TRUE, params = "-PWMATRIX=BLOSUM -TYPE=PROTEIN")
CLUSTAL 2.1 Multiple Sequence Alignments
Sequence type explicitly set to Protein
Sequence format is Pearson
Sequence 1: AT1G01010.1 429 aa
Sequence 2: 333554|PACid_16033839 245 aa
Start of Pairwise alignments
Aligning...
Sequences (1:2) Aligned. Score: 2
Guide tree file created: [/Library/Frameworks/R.framework/Versions/3.1/Resources/library/orthologr/seqs/aa_seqs.dnd]
There are 1 groups
Start of Multiple Alignment
Aligning...
Group 1: Delayed
Alignment Score 29
CLUSTAL-Alignment file created [/var/folders/tb/v6lh8_g505bfjytt3lvdmvw00000gn/T//RtmpOXdtWL/_alignment/multi_aln/clustalw.aln]
[1] "Multiple Alignment successfully written in /var/folders/tb/v6lh8_g505bfjytt3lvdmvw00000gn/T//RtmpOXdtWL/_alignment/multi_aln/clustalw.aln."
AAMultipleAlignment with 2 rows and 429 columns
aln names
[1] MEDQVGFGFRPNDEELVGHYLRNKIEGNTSRDVEVAISEVNICSYD...IKIPPSTNTVKQSWIVLENAQWNYLKNMIIGVLLFISVISWIILVG AT1G01010.1
[2] --------MAASEHRCVGCGFR---------------VKSLFIQYS...IFEP-------TIFLTQFGSLMQYLSYLFRTV-------------- 333554|PACid_1603...
T_COFFEE
system("t_coffee -version")
In case everything is installed appropriately, you should see:
PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 21:55:14 - Revision 8cbe486 - Build 470)
orthologr::multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'), tool = "t_coffee", get_aln = TRUE)
MUSCLE
system("muscle -help")
In case everything is installed appropriately, you should see:
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.
Basic usage
muscle -in <inputfile> -out <outputfile>
Common options (for a complete list please see the User Guide):
-in <inputfile> Input file in FASTA format (default stdin)
-out <outputfile> Output alignment in FASTA format (default stdout)
-diags Find diagonals (faster for similar sequences)
-maxiters <n> Maximum number of iterations (integer, default 16)
-maxhours <h> Maximum time to iterate in hours (default no limit)
-html Write output in HTML format (default FASTA)
-msf Write output in GCG MSF format (default FASTA)
-clw Write output in CLUSTALW format (default FASTA)
-clwstrict As -clw, with 'CLUSTAL W (1.81)' header
-log[a] <logfile> Log to file (append if -loga, overwrite if -log)
-quiet Do not write progress messages to stderr
-version Display version information and exit
Without refinement (very fast, avg accuracy similar to T-Coffee): -maxiters 2
Fastest possible (amino acids): -maxiters 1 -diags -sv -distance1 kbit20_3
Fastest possible (nucleotides): -maxiters 1 -diags
# in case the default execution path of muscle runs properly on your system multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'), tool = "muscle", get_aln = TRUE)
ClustalO
system("clustalo --help")
# in case the default execution path of muscle runs properly on your system multi_aln(file = system.file('seqs/aa_seqs.fasta', package = 'orthologr'), tool = "clustalo", get_aln = TRUE)
MAFFT
system("mafft -help")
In case everything is installed appropriately, you should see:
------------------------------------------------------------------------------ MAFFT v7.187 (2014/10/02) http://mafft.cbrc.jp/alignment/software/ MBE 30:772-780 (2013), NAR 30:3059-3066 (2002) ------------------------------------------------------------------------------ High speed: % mafft in > out % mafft --retree 1 in > out (fast) High accuracy (for <~200 sequences x <~2,000 aa/nt): % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok) % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out) % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out) If unsure which option to use: % mafft --auto in > out --op # : Gap opening penalty, default: 1.53 --ep # : Offset (works like gap extension penalty), default: 0.0 --maxiterate # : Maximum number of iterative refinement, default: 0 --clustalout : Output: clustal format, default: fasta --reorder : Outorder: aligned, default: input order --quiet : Do not report progress --thread # : Number of threads (if unsure, --thread -1)
The multi_aln() function
The multi_aln() function is an interface function between R and common multiple sequence alignment tools. When working with this function a new folder named _alignment is being created and stores the multiple alignment returned by the corresponding alignment tool. The argument get_aln = TRUE allows to work with the multiple alignment generated by the corresponding alignment tool within the current R session.
This small pairwise alignment example shall illustrate how the multi_aln() output can be used:
multi_aln(system.file('seqs/aa_seqs.fasta', package = 'orthologr'), tool = "clustalw", get_aln = TRUE)
$nb [1] 2 $nam [1] "AT1G01010.1" "333554|PACid_16033839" $seq $seq[[1]] [1] "medqvgfgfrpndeelvghylrnkiegntsrdvevaisevnicsydpwnlrfqskyksrdamwyffsrrennk gnrqsrttvsgkwkltgesvevkdqwgfcsegfrgkighkrvlvfldgrypdktksdwvihefhydllpehqrtyvic rleykgddadilsayaidptpafvpnmtssagsvvnqsrqrnsgsyntyseydsanhgqqfnensnimqqqplqgsfn plleydfanhggqwlsdyidlqqqvpylapyenesemiwkhvieenfeflvdertsmqqhysdhrpkkpvsgvlpdds sdtetgsmifedtssstdsvgssdepghtriddipslniieplhnykaqeqpkqqskekvissqksecewkmaedsik ippstntvkqswivlenaqwnylknmiigvllfisviswiilvg" $seq[[2]] [1] "--------maasehrcvgcgfr---------------vkslfiqyspgnirlmk------------------- ---------------cgnckevadey----------iecermiifid---------------------lilhrpkvyr hvlynainpetvniqhllwklvfvyllldsyrslllrrtdeess----------------fshssvlisikvligvls anaafifs----------------------------------------faiaakgllnevs---rgreimlgicissy fkifllamlvwefp----------------msvifivdilvltsnsmalkvmtestmtrciavcliahlvrfsvgqif ep-------tifltqfgslmqylsylfrtv--------------" $com [1] NA attr(,"class") [1] "alignment"
Furthermore, multiple alignments are returned as follows:
multi_aln(system.file('seqs/multi_aln_example.fasta', package = 'orthologr'), tool = "clustalw", get_aln = TRUE)
CLUSTAL 2.1 Multiple Sequence Alignments $nb [1] 4 $nam [1] "AT1G01010.1|PACid_19656964" "Thhalv10006531m|PACid_20187082" [3] "Bra032623|PACid_22715924" "311315|PACid_16059488" $seq $seq[[1]] [1] "----------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- -----------------------------------------medqvgfg------------------frp ndeelvghylrnkiegntsr----------dvevaisevnicsydp---------wnlrfqskyksrd-- -------amwyffsrre------------nnkgnrqsrttvsgkwkltgesvevkdqwgfcseg------ --frgkig-------------------------------------------hkrvlvfldgrypdktksd wvihefhydllpehqr-----------------tyvicr--leykgddadilsayaidptpafvpnmtss agsvvnqsrqrnsgsyntyseydsanhgqqfnensn-imqqqplqgsfnplleydfanhg-------gqw l----------------------------sdyidlqqqvpylapye------------------------ -----------------------------------nesemiwkhvieenfeflvdertsmqqhysdhrpk kpvsgvlp----------------ddssdtetgsmifedtssstds------------------------ ---------------------------------vgssdepghtriddipslniieplhnykaqeqpkqqs kekvissqksecewkmaeds---------ikippstntvkqswivlenaqwnylknmiigvllfisvisw iilvg-------------------------------" $seq[[2]] [1] "mvmederrgdikppsywldacediscdliddlvsdfdpssvavaesvdengvnndffggidhild siknggglpnrahingvsetnsqringnsevseaaqliagettvsvkgnvlqkcggkrdevskeegeknr krarvcsyqrersnlsgrgqansregdrfmnrkrtrnwdeaghnkrrdgynyrrdgrdreargywerdkv gsnelvyrsgtweadherdlkkesgrnresdekaeenkskpeehkekvveeqarryqldvleqakaknti afletgagktliailliksihkdltsqnrkmlsvflvpkvplvyqqaevirnqtcfqvghycgemgqdfw darrwqrefeskqvlvmtaqillnilrhsiirmeainllildechhavkkhpyslvmsefyhttpkdkrp aifgmtaspvnlkgvssqvdcaikirnletkldstvctikdrkelekhvpmpseivveydkaatmwslhe kikqmiaaveeaaqassrkskwqfmgardagakdelrqvygvsertesdgaanlihklrainytlaelgq wcaykvaqsfltalqsdervnfqvdvkfqesylsevvsllqcellegaaaekavaelskpengnandeie egelpddhvvsggehvdkvigaavadgkvtpkvqsliklllkyqhtadfraivfvervvaalvlpkvfae lpslgfircasmighnnsqemkssqmqdtiskfrdgqvtllvatsvaeegldirqcnvvmrfdlaktvla yiqsrgrarkpgsdyilmverenvshaaflrnarnseetlrkeaiertdlshlkdssrlisidavpgtvy kveatgamvslnsavglihfycsqlpgdryailrpefsmvkhekpgghteyscrlqlpcnapfeilegpv cssmrlaqqavclagckklhemgaftdmllpdkgsgqdaekadqddegepipgtarhrefypegvadvlk gewilsgkeicessklfhlymysvrcvdsgvskdpfltevsefavlfgneldaevlsmsmdlyvaramit kaslafrgslditesqlssikkfhvrlmsivldvdvepsttpwdpakaylfvpvadnssaepikginwel vekitkttvwdnplqrarpdvylgtnertlggdrreygfgklrhnigfgqkshptygirgavasfdvvra sgllpvrdalekevegdlsqgklmmadgcmvaenllgkivtaahsgkrfyvdsicydmsaetsfprkegy lgpleyntyadyykqkygvdlsckqqplikgrgvsycknllsprfeqsgesetildktyyvflppelcvv hplsgslvrgaqrlpsimrrvesmllavqlknlisypiptskilealtaascqetfcyeraellgdaylk wivsrflflkypqkhegqltrmrqqmvsnlvlyqyalvkglqsyiqadrfapsrwsapgvppvydedtkd ggssffdeeekpegnkdvfedgemedgelegdlssyrvlssktladvvealigvyyveggktaanhlmkw igihveddpeetegsvkpvynvpesvlksidfvgleralkyeftekgllveaithasrpssgvscyqrle fvgdavldhlitrhlfftytslppgrltdlraaavnnenfarvavkhklhlylrhgssalekqirdfvke vltesskpgfnsfglgdckapkvlgdivesiagaifldsgkdttaawkvfqpllqpmvtpetlpmhpvre lqercqqqaegleykasrsgntatvevfidgvqvgaaqnpqkkmaqklaarnalaalkekeaeeskkkqa ngnaagenqddnengnkkngnqtftrqtlndiclrknwpmpsyrcvkeggpahakrftfgvrvntsdrgw tdecigepmpsvkkakdsaailllellnktys----" $seq[[3]] [1] "----------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- -----------------------------------------------mqqppqmfpmapsmpptnitteq iqkyleenkklimaimenqnlgklaecaqyqallqknlmylaaiadaqpppstagatppp---------- ---------------------------------amasqmgaphpg------------------------- ---------------------------------------------mqppsyfmqhp------qasgmaqq appagifp----------------------prgplqfgsphqlqdp------------------------ -----------------------------------qqqhmhqqamqghmgmrpmginnnngmqhqmqqqp etslggsaanvgirggkqdg-------------------------adgqgkddgk--------------- ------------------------------------" $seq[[4]] [1] "----------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- ---------------------------------------------------------------------- --------------------------------------------------------mlslnmrteienlw vfalaskfnifmqehfaslllaiaitwctltivfwstpggpawg-------------------------- --------------------------kyfftrrfsslghnrksknlipgprgfplvgsmslrsshvahqr iasvaemsnakrlmafslgdtkvvvtchpdvakeilnssvfadrpvdetayg---lmfnramgfapngty wrtlrrlssnhlfnpkqikrseeqrrviatqmvnafarnaksafavrdllktaslcnmmglvfg------ -----------------------------------------------------reyelesnnnveseclk glveegydllg-----------------------tlnwtdhlpwlagldfqqirfrcsqlvpkvnlllsr iihehyatgnfldvllslqrseklsdsdivavlwemifrgtdtvavliewvlarialhpk---------- ----------------------------------vqstvhdeldr------------------------- ---------------------------------------------vvgrsrtvdesdlpsltyltamike vlr--lhp-----------------------pgpllswarlsitdt------------------------ ------------------------------------tvdgyhvpagttamvnmwaiardphvwedplefk perfvakdgeaefsvfgsdlr---------------lapfgsgkrvcpgknlglttvsfwvatllhefew lpsveanppdlsevlrlscemacplivnvsprrksv" $com [1] NA attr(,"class") [1] "alignment"
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