Index

Symbols

--append seqExtract command line option --check-all stopCleaner command line option --check-alphabet stopCleaner command line option --check-duplications stopCleaner command line option --check-stops stopCleaner command line option --column <ARG> seqExtract command line option --comment isoformCleaner command line option --d1 <DOMAIN> dsmReader command line option --d2 <DOMAIN> dsmReader command line option --delim-extract <ARG> seqExtract command line option --delim-pos <ARG> seqExtract command line option --domains <FILE> extractDomains command line option --extract-order seqExtract command line option --fix-and-keep stopCleaner command line option --fix-and-remove stopCleaner command line option --fix-ending stopCleaner command line option --help dsmReader command line option extractDomains command line option isoformCleaner command line option seqExtract command line option stopCleaner command line option --id <ARG> extractDomains command line option --ignore-missing <ARG> seqExtract command line option --in isoformCleaner command line option stopCleaner command line option --in <FILE> seqExtract command line option --index seqExtract command line option --indexFile <FILE> seqExtract command line option --inputList <FILE> seqExtract command line option --length <ARG> seqExtract command line option --matrix <FILE> dsmReader command line option --min-length <ARG> extractDomains command line option --name isoformCleaner command line option --name <ARG> extractDomains command line option --namesFile <FILE> seqExtract command line option --numSeqs <ARG> seqExtract command line option --out <FILE> extractDomains command line option isoformCleaner command line option seqExtract command line option stopCleaner command line option --preset <ARG> isoformCleaner command line option --regular <ARG> isoformCleaner command line option --remove seqExtract command line option --remove-alpha stopCleaner command line option --remove-comments seqExtract command line option --remove-duplicates stopCleaner command line option --remove-stop-genes stopCleaner command line option --rename-duplicates stopCleaner command line option --replace-char stopCleaner command line option --replace-stop stopCleaner command line option --report <FILE> stopCleaner command line option --revComp seqExtract command line option

--seed <ARG> seqExtract command line option --sequences <FILE> extractDomains command line option --set-alphabet stopCleaner command line option --split-char <CHAR> isoformCleaner command line option --stop-char stopCleaner command line option --summary isoformCleaner command line option --table <ARG> seqExtract command line option --translate seqExtract command line option --use-evelope extractDomains command line option --use-negative dsmReader command line option -A stopCleaner command line option -a seqExtract command line option -c isoformCleaner command line option seqExtract command line option -C <ARG> seqExtract command line option -D <ARG> seqExtract command line option -d <ARG> seqExtract command line option -d <FILE> extractDomains command line option -e extractDomains command line option -e <ARG> --extract <ARG> seqExtract command line option -F <FILE> seqExtract command line option -h dsmReader command line option extractDomains command line option isoformCleaner command line option seqExtract command line option stopCleaner command line option -I seqExtract command line option -i <FILE> isoformCleaner command line option seqExtract command line option stopCleaner command line option -L <ARG> seqExtract command line option -l <FILE> seqExtract command line option -m <ARG> seqExtract command line option -m <FILE> dsmReader command line option -n dsmReader command line option isoformCleaner command line option -n <ARG> extractDomains command line option seqExtract command line option -N <FILE> seqExtract command line option -o <FILE> extractDomains command line option isoformCleaner command line option seqExtract command line option stopCleaner command line option -p <ARG> isoformCleaner command line option -R seqExtract command line option -r seqExtract command line option -r <ARG> isoformCleaner command line option -r <FILE> stopCleaner command line option -s <ARG> seqExtract command line option -s <CHAR> isoformCleaner command line option -s <FILE> extractDomains command line option -t seqExtract command line option -T <ARG> seqExtract command line option

D

dsmReader command line option --d1 <DOMAIN> --d2 <DOMAIN> --help --matrix <FILE> --use-negative -h -m <FILE> -n

E

extractDomains command line option --domains <FILE> --help --id <ARG> --min-length <ARG> --name <ARG> --out <FILE> --sequences <FILE> --use-evelope -d <FILE> -e -h -n <ARG> -o <FILE> -s <FILE>

I

isoformCleaner command line option --comment --help --in --name --out <FILE> --preset <ARG> --regular <ARG> --split-char <CHAR> --summary -c -h -i <FILE> -n -o <FILE> -p <ARG> -r <ARG> -s <CHAR>

S

seqExtract command line option --append --column <ARG> --delim-extract <ARG> --delim-pos <ARG> --extract-order --help --ignore-missing <ARG> --in <FILE> --index --indexFile <FILE> --inputList <FILE> --length <ARG> --namesFile <FILE> --numSeqs <ARG> --out <FILE> --remove --remove-comments --revComp --seed <ARG> --table <ARG> --translate -a -c -C <ARG> -d <ARG> -D <ARG> -e <ARG> --extract <ARG> -F <FILE> -h -I -i <FILE> -L <ARG> -l <FILE> -m <ARG> -n <ARG> -N <FILE> -o <FILE> -r -R -s <ARG> -t -T <ARG>

stopCleaner command line option --check-all --check-alphabet --check-duplications --check-stops --fix-and-keep --fix-and-remove --fix-ending --help --in --out <FILE> --remove-alpha --remove-duplicates --remove-stop-genes --rename-duplicates --replace-char --replace-stop --report <FILE> --set-alphabet --stop-char -A -h -i <FILE> -o <FILE> -r <FILE>