True False

yes no yes no

1 2 3 4 5 6 7 8 9

all ortholog_one2one apparent_ortholog_one2one ortholog_one2many ortholog_many2many between_species_paralog within_species_paralog

true false

chr10 chr13 chr16 chr19 chr21 chr3 chr6 chr9 chrY chr11 chr14 chr17 chr1 chr22 chr4 chr7 chrM chr12 chr15 chr18 chr20 chr2 chr5 chr8 chrX

on off BLOSUM PAM GONNET ID IUB CLUSTALW

BLOSUM PAM GONNET ID IUB CLUSTALW BLOSUM PAM GONNET ID IUB CLUSTALW on off

BLOSUM62 BLOSUM50 BLOSUM40 PAM250 PAM100 PAM50 DNAFULL DNAMAT

0.0 100.0 0.0 10.0

Trypsin Lys-C Arg-C Asp-N V8-bicarb V8-phosph Chymotrypsin CNBr

Trypsin Lys-C Arg-C Asp-N V8-bicarb V8-phosph Chymotrypsin CNBr pdbaa nr swissprot trembl

yes no 0 1 2 3 4 5 6 yes no 0 1 2 3 4 5 6 9 10 11 12 13 14 15 16 21 22 23 yes no

BLOSUM62 BLOSUM50 BLOSUM40 PAM250 PAM100 PAM50 DNAFULL DNAMAT

yes no 1 200 yes no yes no

swissprot trembl nr pdb

yes no

yes no yes no yes no yes no yes no yes no yes no

F I P V O

yes no yes no 1 2 3 F -1 -2 -3 R 6 yes no

BLOSUM62 BLOSUM50 BLOSUM40 PAM250 PAM100 PAM50 DNAFULL DNAMAT

UniProt PDB Swiss-Prot TrEMBL 1 2 PAM250 PAM120 PAM20 PAM40 MDM10 MDM20 MDM40 BLOSUM50 BLOSUM62 BLOSUM80

GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral

PAM250 PAM120 PAM20 PAM40 MDM10 MDM20 MDM40 BLOSUM50 BLOSUM62 BLOSUM80 1 2 UniProt PDB Swiss-Prot TrEMBL

UniProt PDB Swiss-Prot TrEMBL 1 2 PAM250 PAM120 PAM20 PAM40 MDM10 MDM20 MDM40 BLOSUM50 BLOSUM62 BLOSUM80

1 2 UniProt PDB Swiss-Prot TrEMBL PAM250 PAM120 PAM20 PAM40 MDM10 MDM20 MDM40 BLOSUM50 BLOSUM62 BLOSUM80

false true none multiple_local_alignments single_global_alignments single_local_alignments wblosum wme wgsc

on off

Swiss-Prot TrEMBL PDB

true false

false true PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 blastp blastn blastx tblastn tblastx true false

false true PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 blastp blastn blastx tblastn tblastx true false

true false RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT false true

false true RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT true false

true false false true

false true PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 uniref90 TrEMBL Swiss-Prot UniProt PDB nr RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral true false

false true PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 TrEMBL Swiss-Prot UniProt PDB nr RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral true false

true false PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 false true

true false false true PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 TrEMBL Swiss-Prot UniProt PDB nr RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral

false true PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 TrEMBL Swiss-Prot UniProt PDB nr RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral true false

PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 false true true false

True False protein dna

PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT false true true false

false true PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT true false

PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 true false false true

true false false true PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT

false true PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT true false

true false PAM30 PAM70 BLOSUM45 BLOSUM62 BLOSUM80 false true

yes no

square lower-triangular yes no Kimura Jukes-Cantor ML JinNei

yes no yes no yes no yes no

yes no yes no yes no

yes no yes no

yes no yes no

yes no yes no lower-triangular upper-triangular square yes no yes no yes no

yes no yes no yes no lower-triangular upper-triangular square

yes no neighbor-joining UPGMA yes no lower-triangular upper-triangular square yes no

PAM Kimura Category_model G(George/Hunt/Barker) C(Chemical) H(Hall) U(Universal) M(Mitochondrial) V(Vertebrate_mitochondrial) F(Fly_mitochondrial) Y(Yeast_mitochondrial)

yes no yes no

ON OFF ON OFF

yes no yes no

yes no yes no yes no

GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral 1 2 PAM250 PAM120 PAM20 PAM40 MDM10 MDM20 MDM40 BLOSUM50 BLOSUM62 BLOSUM80

1 2 GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral PAM250 PAM120 PAM20 PAM40 MDM10 MDM20 MDM40 BLOSUM50 BLOSUM62 BLOSUM80

slow_triplet fast_triplet very_fast_triplet 0 1 off on cfasta_pair_wise myers_miller_pair_wise gotoh_pair_wise fasta_pair_wise slow fast fast_pair and lalign_id_pair fast_pair lalign_id_pair slow_pair

none seg dust sump poissonp kap RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT off on

sump poissonp kap none seg dust off on

none seg xnu seg+xnu sump poissonp kap blosum30 blosum35 blosum40 blosum45 blosum50 blosum65 blosum70 blosum75 blosum80 blosum85 blosum90 blosum100 pam10 pam20 pam30 pam40 pam50 pam60 pam70 pam80 pam90 pam100 pam110 pam120 pam130 pam140 pam150 pam160 pam170 pam180 pam190 pam200 pam210 pam220 pam230 pam240 pam250 pam260 pam270 pam280 pam290 pam300 pam310 pam320 pam330 pam340 pam350 pam360 pam370 pam380 pam390 pam400 pam410 pam420 pam430 pam440 pam450 pam460 pam470 pam480 pam490 pam500 UniProt Swiss-Prot TrEMBL off on

off on none seg xnu seg+xnu sump poissonp kap blosum30 blosum35 blosum40 blosum45 blosum50 blosum65 blosum70 blosum75 blosum80 blosum85 blosum90 blosum100 pam10 pam20 pam30 pam40 pam50 pam60 pam70 pam80 pam90 pam100 pam110 pam120 pam130 pam140 pam150 pam160 pam170 pam180 pam190 pam200 pam210 pam220 pam230 pam240 pam250 pam260 pam270 pam280 pam290 pam300 pam310 pam320 pam330 pam340 pam350 pam360 pam370 pam380 pam390 pam400 pam410 pam420 pam430 pam440 pam450 pam460 pam470 pam480 pam490 pam500

none seg xnu seg+xnu sump poissonp kap blosum30 blosum35 blosum40 blosum45 blosum50 blosum65 blosum70 blosum75 blosum80 blosum85 blosum90 blosum100 pam10 pam20 pam30 pam40 pam50 pam60 pam70 pam80 pam90 pam100 pam110 pam120 pam130 pam140 pam150 pam160 pam170 pam180 pam190 pam200 pam210 pam220 pam230 pam240 pam250 pam260 pam270 pam280 pam290 pam300 pam310 pam320 pam330 pam340 pam350 pam360 pam370 pam380 pam390 pam400 pam410 pam420 pam430 pam440 pam450 pam460 pam470 pam480 pam490 pam500 UniProt Swiss-Prot TrEMBL off on

sump poissonp kap none seg xnu seg+xnu off on blosum30 blosum35 blosum40 blosum45 blosum50 blosum65 blosum70 blosum75 blosum80 blosum85 blosum90 blosum100 pam10 pam20 pam30 pam40 pam50 pam60 pam70 pam80 pam90 pam100 pam110 pam120 pam130 pam140 pam150 pam160 pam170 pam180 pam190 pam200 pam210 pam220 pam230 pam240 pam250 pam260 pam270 pam280 pam290 pam300 pam310 pam320 pam330 pam340 pam350 pam360 pam370 pam380 pam390 pam400 pam410 pam420 pam430 pam440 pam450 pam460 pam470 pam480 pam490 pam500

none seg xnu seg+xnu sump poissonp kap blosum30 blosum35 blosum40 blosum45 blosum50 blosum65 blosum70 blosum75 blosum80 blosum85 blosum90 blosum100 pam10 pam20 pam30 pam40 pam50 pam60 pam70 pam80 pam90 pam100 pam110 pam120 pam130 pam140 pam150 pam160 pam170 pam180 pam190 pam200 pam210 pam220 pam230 pam240 pam250 pam260 pam270 pam280 pam290 pam300 pam310 pam320 pam330 pam340 pam350 pam360 pam370 pam380 pam390 pam400 pam410 pam420 pam430 pam440 pam450 pam460 pam470 pam480 pam490 pam500 RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT off on

sump poissonp kap none seg xnu seg+xnu off on blosum30 blosum35 blosum40 blosum45 blosum50 blosum65 blosum70 blosum75 blosum80 blosum85 blosum90 blosum100 pam10 pam20 pam30 pam40 pam50 pam60 pam70 pam80 pam90 pam100 pam110 pam120 pam130 pam140 pam150 pam160 pam170 pam180 pam190 pam200 pam210 pam220 pam230 pam240 pam250 pam260 pam270 pam280 pam290 pam300 pam310 pam320 pam330 pam340 pam350 pam360 pam370 pam380 pam390 pam400 pam410 pam420 pam430 pam440 pam450 pam460 pam470 pam480 pam490 pam500

none seg xnu seg+xnu sump poissonp kap blosum30 blosum35 blosum40 blosum45 blosum50 blosum65 blosum70 blosum75 blosum80 blosum85 blosum90 blosum100 pam10 pam20 pam30 pam40 pam50 pam60 pam70 pam80 pam90 pam100 pam110 pam120 pam130 pam140 pam150 pam160 pam170 pam180 pam190 pam200 pam210 pam220 pam230 pam240 pam250 pam260 pam270 pam280 pam290 pam300 pam310 pam320 pam330 pam340 pam350 pam360 pam370 pam380 pam390 pam400 pam410 pam420 pam430 pam440 pam450 pam460 pam470 pam480 pam490 pam500 RefSeq RefSeq fungi RefSeq invertebrate RefSeq microbial RefSeq mitochondrion RefSeq plant RefSeq plasmid RefSeq plastid RefSeq protozoa RefSeq vertebrate_mammalian RefSeq vertebrate_other RefSeq viral GenBank GenBank BCT GenBank ENV GenBank EST GenBank GSS GenBank HTC GenBank HTG GenBank INV GenBank MAM GenBank PAT GenBank PHG GenBank PLN GenBank PRI GenBank ROD GenBank STS GenBank SYN GenBank UNA GenBank VRL GenBank VRT off on

off on blosum30 blosum35 blosum40 blosum45 blosum50 blosum65 blosum70 blosum75 blosum80 blosum85 blosum90 blosum100 pam10 pam20 pam30 pam40 pam50 pam60 pam70 pam80 pam90 pam100 pam110 pam120 pam130 pam140 pam150 pam160 pam170 pam180 pam190 pam200 pam210 pam220 pam230 pam240 pam250 pam260 pam270 pam280 pam290 pam300 pam310 pam320 pam330 pam340 pam350 pam360 pam370 pam380 pam390 pam400 pam410 pam420 pam430 pam440 pam450 pam460 pam470 pam480 pam490 pam500 sump poissonp kap none seg xnu seg+xnu

yes no yes no yes no yes no yes no yes no yes no yes no yes no yes no yes no yes no yes no yes no yes no

True False