AB Bootstrap - mendessoares/BuddySuite GitHub Wiki

--bootstrap, -bts

Description

Create new alignments by sampling columns from the original alignment with replacement. The new alignment(s) will be the same length as the original. If multiple alignments are given as input, bootstrap alignments will be made for each separately.

Arguments

'number bootstraps' ( int )

Optional. By default, only a single bootstrap alignment will be generated for each input alignment. Create more by passing in an integer.

Examples

Input file: Panxs.phy

 5 50
Mle-Panxα1    MYWIFE-----------ICQEIKRAQSCRKFAIDGPFDWTNRIIMPTLMV
Mle-Panxα12   M--VID-----------ILSGFKGITPFKGITLDDGWDQINRSFMFVLCV
Mle-Panxα11   M--LIS-----------SLVQFSRLSPFKEITIDDGWDQLNRSFMFVLMV
Mle-Panxα10B  M-RLSEKSTSHDCKACITRSHNEDCARRWGITIDDGWDQLNRSFMFGLLV
Mle-Panxα10A  M-RLSEKSTSHDCKACITRSHNEDCARRWGITIDDGWDQLNRSFMFGLLV

 5 50
Ael_PanxβA___CDS  -----------------------------MVVIRELKDILSMKIKTRHDG
Ael_PanxβB___CDS  -----------------------------MVVIRGLKDILSIKMKTRHDS
Ael_PanxβC___CDS  MPNNIYPNRLFVKTNDIPEKLNTPWSYEKMVVVRVLKDILSIKIKPRHDG
Ael_PanxβD___CDS  --------------------------------MEVLKDILSVQLKSRDDS
Ael_PanxβE___CDS  ------------------------------MIGDAISNIISIKIKHRDDG

Usage example 1

$: alb Panxs.phy -bts

Output

 5 50
Mle-Panxα1    QWWFCEFIIIILV-AQA-I-D-VDD--IE---CLRDW-TC--TPVQIF--
Mle-Panxα12   S--ILGIFSFFLV-IST-F-D-VDD--FD---FLKD--VL--VGVTII--
Mle-Panxα11   V--ILQIFSFFLV-LVT-F-D-VDD--FS---FLKD--VL--VGVSSI--
Mle-Panxα10B  SRRIRHSFSFFLVACSTAFADDVDDDSFESAHRLWDRCGRTKGGVATSIS
Mle-Panxα10A  SRRIRHSFSFFLVACSTAFADDVDDDSFESAHRLWDRCGRTKGGVATSIS

 5 50
Ael_PanxβA___CDS  --V-TM-K---TK--IKHDKIE-----R-D-K---K-H--D-RD-KIR--
Ael_PanxβB___CDS  --V-TM-K---TK--IKHDKMG-----R-D-K---K-H--D-RD-KMR--
Ael_PanxβC___CDS  WIVTPMEKPYPPKPIIKHDKIVPNKNPREDTKTTKKEHVPDYRDYKIRKL
Ael_PanxβD___CDS  ----S--K---SK--IKDDKLV-----R-D-K---K-D--D-ED-KLE--
Ael_PanxβE___CDS  --M-H--K---HK--IKDNSIA-----R-N-K---S-D--N-DD-KID--

Usage example 2

$: alb Panxs.phy -bts 3

Output

 5 50
Mle-Panxα1    DC-I-ARAI-QLRYMIPKEPRLI-PI-WIIK-Q-TM-KKLPFYFRW-DR-
Mle-Panxα12   DF-F-IRIV-TLR-MSFGGFKLL-GF--IFG-S-IM-KGLFI-WK--DR-
Mle-Panxα11   DF-F-LRLL-SLR-MSFEQFKLI-GF--SFE-V-LM-SELFI-WK--DR-
Mle-Panxα10B  DRHNSCRCLKALR-MSFGHFWLITGNTRTNGISHLMDEGLFS-WWRSDRS
Mle-Panxα10A  DRHNSCRCLKALR-MSFGHFWLITGNTRTNGISHLMDEGLFS-WWRSDRS

 5 50
Mle-Panxα1    -MGMPPGGAELT-QAIKLIFQ-M--SEMI-F-IIIM-ERIWMMI--CDFD
Mle-Panxα12   -MDCGFDDIDLI-STFGLFIS-M--PGML-I-FSFM-DGL-MCV--LDWD
Mle-Panxα11   -MDMGFDDLSLL-VTFELFIV-M--PQMI-I-FSFM-SRI-MML--LDWD
Mle-Panxα10B  DMDLGFDDCELLKSTNGLNSSAMAARHMIHICNSNMTEDIRMLLDSRDWD
Mle-Panxα10A  DMDLGFDDCELLKSTNGLNSSAMAARHMIHICNSNMTEDIRMLLDSRDWD

 5 50
Mle-Panxα1    NRF---F--F--PM-MR-D-TITEIVD-AI-AR---TY---EFN-YAAL-
Mle-Panxα12   NGI---I--I--GM-MR-D-IFIGIVD-TV-TG---V----GIN--TTL-
Mle-Panxα11   NRI---I--I--GM-MR-D-LFLQSVD-TL-TR---V----QIN--TTL-
Mle-Panxα10B  NDSAATSCKICDGMTMRSDILFLHTVDKTLCTDCDIG-HHKHINA-TTLT
Mle-Panxα10A  NDSAATSCKICDGMTMRSDILFLHTVDKTLCTDCDIG-HHKHINA-TTLT

 5 50
Ael_PanxβA___CDS  ---------D--E--IVEM-H--------K----D-K--V-LML--RR--
Ael_PanxβB___CDS  ---------D--G--IVGM-H--------K----D-K--V-LML--RR--
Ael_PanxβC___CDS  YYNEKKLYWDPPVNNVVVMMHPRPNFPRPKNPTRDTKYKVNLMLFERRYF
Ael_PanxβD___CDS  ---------D--V--M-V--D--------Q----D-Q----L-L--ER--
Ael_PanxβE___CDS  ---------D--A--GIA--D--------K----D-K--M-I-I--DR--

 5 50
Ael_PanxβA___CDS  --GV--M-HKMKK---I-----V-R-HD-----I-E------HELDIS-G
Ael_PanxβB___CDS  --SV--I-HKMKK---M-----V-R-HD-----I-G------HGLDMS-S
Ael_PanxβC___CDS  NPGVNEIIHKMKKPKNINPENTVKRTHDINNVVVDVLLIKKLHVLDISMG
Ael_PanxβD___CDS  --S---V-DK-KK---L-------E-DD-----M-V------DVLDLS-S
Ael_PanxβE___CDS  --GM--I-DK-SK---I-----I-D-DN-----G-A------DAIDIS-G

 5 50
Ael_PanxβA___CDS  V--I--V-----S---T-V------MLLD---VH----E-RV--L---H-
Ael_PanxβB___CDS  V--I--V-----S---T-V------ILLD---VH----G-RV--L---H-
Ael_PanxβC___CDS  VFMINTVINWLLSTTLPFVPRLKNEILLDEMFVHLNEPVERVKILKFWHT
Ael_PanxβD___CDS  ---I--------S---S--------VLLD----D----V-R---L---D-
Ael_PanxβE___CDS  M--I--M-----S---H-M------IIID---ID----A-RM--I---D-