IdClusters: Cluster Sequences By Distance or Sequence

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/IdClusters.R

Description

Groups the sequences represented by a distance matrix into clusters of similarity.

Usage

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IdClusters(myDistMatrix = NULL,
           method = "UPGMA",
           cutoff = -Inf,
           showPlot = FALSE,
           type = "clusters",
           myXStringSet = NULL,
           model = MODELS,
           collapse = 0,
           processors = 1,
           verbose = TRUE)

Arguments

myDistMatrix

A symmetric N x N distance matrix with the values of dissimilarity between N sequences, or NULL if method is "inexact".

method

An agglomeration method to be used. This should be (an abbreviation of) one of "complete", "single", "UPGMA", "WPGMA", "NJ", "ML", or "inexact". (See details section below.)

cutoff

A vector with the maximum edge length separating the sequences in the same cluster. Multiple cutoffs may be provided in ascending or descending order. (See details section below.)

showPlot

Logical specifying whether or not to plot the resulting dendrogram. Not applicable if method='inexact'.

type

Character string indicating the type of output desired. This should be (an abbreviation of) one of "clusters", "dendrogram", or "both". Not applicable if method='inexact'. (See value section below.)

myXStringSet

If method is "ML", the DNAStringSet or RNAStringSet used in the creation of myDistMatrix. If method is "inexact", the DNAStringSet, RNAStringSet, or AAStringSet to cluster. Not applicable for other methods.

collapse

Numeric controlling which internal edges of the tree are removed by collapsing their nodes. If collapse is zero (the default) then nodes at the same height will be collapsed to a single node, resulting in a multifurcating tree. When collapse is greater than zero, nodes that are within collapse difference in height are made into a single node. A value of collapse less than zero will ensure that the dendrogram is purely bifurcating. Note that collapse has no effect on cluster numbers or cutoff.

model

One or more of the available MODELS of DNA evolution. Only applicable if method is "ML".

processors

The number of processors to use, or NULL to automatically detect and use all available processors.

verbose

Logical indicating whether to display progress.

Details

IdClusters groups the input sequences into clusters using a set dissimilarities representing the distance between N sequences. Initially a phylogenetic tree is formed using the specified method. Then each leaf (sequence) of the tree is assigned to a cluster based on its edge lengths to the other sequences. The available clustering methods are described as follows:

Ultrametric methods: The method complete assigns clusters using complete-linkage so that sequences in the same cluster are no more than cutoff percent apart. The method single assigns clusters using single-linkage so that sequences in the same cluster are within cutoff of at least one other sequence in the same cluster. UPGMA (the default) or WPGMA assign clusters using average-linkage which is a compromise between the sensitivity of complete-linkage clustering to outliers and the tendency of single-linkage clustering to connect distant relatives that do not appear to be closely related. UPGMA produces an unweighted tree, where each leaf contributes equally to the average edge lengths, whereas WPGMA produces a weighted result.

Additive methods: NJ uses the Neighbor-Joining method proposed by Saitou and Nei that does not assume lineages evolve at the same rate (the molecular clock hypothesis). The NJ method is typically the most phylogenetically accurate of the above distance-based methods. ML creates a neighbor-joining tree and then iteratively maximizes the likelihood of the tree given the aligned sequences (myXStringSet). This is accomplished through a combination of optimizing edge lengths with Brent's method and improving tree topology with nearest-neighbor interchanges (NNIs). When method="ML", one or more MODELS of DNA evolution must be specified. Model parameters are iteratively optimized to maximize likelihood, except base frequencies which are empirically determined. If multiple models are given, the best model is automatically chosen based on BIC calculated from the likelihood and the sample size (defined as the number of variable sites in the DNA sequence).

Sequence-only method: inexact uses a heuristic algorithm to directly assign sequences to clusters without a distance matrix. First the sequences are ordered by length and the longest sequence becomes the first cluster seed. If the second sequence is less than cutoff percent distance then it is added to the cluster, otherwise it becomes a new cluster representative. The remaining sequences are matched to cluster representatives based on their k-mer distribution and then aligned to find the closest sequence. This approach is repeated until all sequences belong to a cluster. In the vast majority of cases, this process results in clusters with members separated by less than cutoff distance, where distance is defined as the percent dissimilarity between the overlapping region of a “glocal” alignment.

Multiple cutoffs may be provided if they are in increasing or decreasing order. If cutoffs are provided in descending order then clustering at each new value of cutoff is continued within the prior cutoff's clusters. In this way clusters at lower values of cutoff are completely contained within their umbrella clusters at higher values of cutoff. This is useful for defining taxonomy, where lower level groups (e.g., genera) are expected not to straddle multiple higher level groups (e.g., families). If multiple cutoffs are provided in ascending order then clustering at each level of cutoff is independent of the prior level. This may result in fewer high-level clusters for NJ and ML methods, but will have no impact on ultrametric methods. Providing cutoffs in descending order makes inexact clustering faster, but has negligible impact on the other methods.

Value

If type is "clusters" (the default), then a data.frame is returned with a column for each cutoff specified. This data.frame has dimensions N*M, where each one of N sequences is assigned to a cluster at the M-level of cutoff. The row.names of the data.frame correspond to the dimnames of myDistMatrix. If type is "dendrogram", then an object of class dendrogram is returned that can be used for plotting. Leaves of the dendrogram are colored by cluster number. If type is "both" then a list is returned containing both the "clusters" and "dendrogram" outputs.

Author(s)

Erik Wright [email protected]

References

Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17(6), 368-376.

Ghodsi, M., Liu, B., & Pop, M. (2011) DNACLUST. BMC Bioinformatics, 12(1), 271. doi:10.1186/1471-2105-12-271.

Saitou, N. and Nei, M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4(4), 406-425.

See Also

DistanceMatrix, Add2DB, MODELS

Examples

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# using the matrix from the original paper by Saitou and Nei
m <- matrix(0,8,8)
m[2:8,1] <- c(7, 8, 11, 13, 16, 13, 17)
m[3:8,2] <- c(5, 8, 10, 13, 10, 14)
m[4:8,3] <- c(5, 7, 10, 7, 11)
m[5:8,4] <- c(8, 11, 8, 12)
m[6:8,5] <- c(5, 6, 10)
m[7:8,6] <- c(9, 13)
m[8,7] <- c(8)

# returns an object of class "dendrogram"
tree <- IdClusters(m, cutoff=10, method="NJ", showPlot=TRUE, type="dendrogram")

# example of specifying multiple cutoffs
clusters <- IdClusters(m, cutoff=c(2,6,10,20)) # returns a data frame
head(clusters)

# example of 'inexact' clustering
fas <- system.file("extdata", "50S_ribosomal_protein_L2.fas", package="DECIPHER")
dna <- readDNAStringSet(fas)
IdClusters(myXStringSet=dna, method="inexact", cutoff=0.05)

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

Loading required package: RSQLite

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Time difference of 4.36 secs

                                                                cluster
Rickettsia prowazekii str. Dachau                                   102
Porphyromonas gingivalis W83                                         90
Porphyromonas gingivalis TDC60                                       90
Porphyromonas gingivalis ATCC 33277                                  90
Pasteurella multocida 671/90                                        103
Pasteurella multocida 36950                                         103
Xanthomonas campestris pv. campestris                                79
Lactobacillus plantarum subsp. plantarum P-8                         27
Lactobacillus plantarum ZJ316                                        27
Lactobacillus plantarum subsp. plantarum NC8                         27
Lactobacillus plantarum subsp. plantarum ATCC 14917                  27
Lactobacillus plantarum WCFS1                                        27
Xanthomonas citri pv. mangiferaeindicae LMG 941                      80
Xanthomonas axonopodis pv. punicae str. LMG 859                      80
Xanthomonas citri subsp. citri Aw12879                               80
Xanthomonas vesicatoria ATCC 35937                                   80
Xanthomonas fuscans subsp. aurantifolii str. ICPB 11122              80
Xanthomonas fuscans subsp. aurantifolii str. ICPB 10535              80
Xanthomonas campestris pv. vesicatoria str. 85-10                    80
Xanthomonas axonopodis pv. citrumelo F1                              80
Xanthomonas oryzae pv. oryzicola BLS256                              81
Xanthomonas campestris pv. raphani 756C                              79
Bacillus halodurans C-125                                            56
Corynebacterium glutamicum SCgG2                                     20
Corynebacterium glutamicum K051                                      20
Synechocystis sp. PCC 6803 substr. PCC-N                             57
Vibrio parahaemolyticus O1:K33 str. CDC_K4557                        91
Vibrio parahaemolyticus BB22OP                                       91
Vibrio parahaemolyticus 10329                                        91
Streptococcus pyogenes SSI-1                                        115
Lactococcus lactis subsp. lactis IO-1                                58
Lactococcus lactis subsp. lactis bv. diacetylactis str. LD61         58
Lactococcus lactis subsp. cremoris CNCM I-1631                       58
Lactococcus lactis subsp. lactis KF147                               58
Clostridium perfringens F262                                         41
Clostridium perfringens D str. JGS1721                               41
Clostridium perfringens SM101                                        41
Mycoplasma pneumoniae M129-B7                                         4
Streptomyces avermitilis MA-4680                                     32
Treponema pallidum subsp. pallidum str. Nichols                     104
Helicobacter pylori X47-2AL                                          59
Helicobacter pylori G27                                              60
Helicobacter pylori XZ274                                            61
Helicobacter pylori Shi417                                           61
Helicobacter pylori UM032                                            61
Helicobacter pylori Aklavik86                                        61
Helicobacter pylori 83                                               61
Helicobacter pylori Hp M3                                            62
Helicobacter pylori Hp P-15b                                         60
Helicobacter pylori Hp P-4d                                          62
Helicobacter pylori Hp P-62                                          62
Helicobacter pylori Hp P-30                                          60
Helicobacter pylori Hp P-3                                           62
Helicobacter pylori Hp H-23                                          62
Helicobacter pylori Hp H-19                                          62
Helicobacter pylori Hp H-18                                          62
Helicobacter pylori Hp H-11                                          59
Helicobacter pylori Hp A-16                                          62
Helicobacter pylori Hp H-44                                          62
Helicobacter pylori Hp H-41                                          62
Helicobacter pylori Hp H-27                                          59
Helicobacter pylori CPY6311                                          61
Helicobacter pylori CPY1313                                          61
Helicobacter pylori NQ4216                                           59
Helicobacter pylori Hp H-16                                          62
Helicobacter pylori Hp H-9                                           59
Helicobacter pylori Hp H-30                                          62
Helicobacter pylori Hp P-11                                          62
Helicobacter pylori CPY1962                                          59
Helicobacter pylori Hp H-4                                           62
Helicobacter pylori Hp H-5b                                          62
Helicobacter pylori CPY1124                                          59
Helicobacter pylori Hp H-42                                          62
Helicobacter pylori Hp H-36                                          62
Helicobacter pylori Hp H-10                                          62
Helicobacter pylori Hp P-74                                          59
Helicobacter pylori NQ4044                                           60
Helicobacter pylori Hp A-26                                          60
Helicobacter pylori CPY6081                                          59
Helicobacter pylori CPY3281                                          61
Helicobacter pylori NQ4200                                           59
Helicobacter pylori Hp A-8                                           62
Helicobacter pylori NQ4053                                           62
Helicobacter pylori Hp P-26                                          62
Helicobacter pylori CPY6261                                          59
Helicobacter pylori B128                                             62
Helicobacter pylori 98-10                                            61
Helicobacter pylori Hp A-6                                           62
Helicobacter pylori ELS37                                            59
Helicobacter pylori Puno135                                          59
Helicobacter pylori Puno120                                          59
Helicobacter pylori Gambia94/24                                      62
Helicobacter pylori 2017                                             62
Helicobacter pylori Sat464                                           59
Helicobacter pylori 908                                              62
Helicobacter pylori v225d                                            59
Helicobacter pylori J99                                              60
Helicobacter pylori P12                                              59
Helicobacter pylori F57                                              59
Helicobacter pylori F32                                              61
Helicobacter pylori F16                                              63
Helicobacter pylori Rif2                                             59
Helicobacter pylori PeCan18                                          64
Helicobacter pylori Hp P-13b                                         62
Helicobacter pylori Hp P-16                                          60
Helicobacter pylori Hp H-43                                          62
Helicobacter pylori Hp A-9                                           59
Helicobacter pylori Hp A-27                                          59
Helicobacter pylori Hp A-14                                          60
Helicobacter pylori Hp H-28                                          59
Helicobacter pylori NQ4110                                           59
Helicobacter pylori Hp H-45                                          62
Helicobacter pylori Lithuania75                                      59
Helicobacter pylori SJM180                                           62
Helicobacter pylori HPAG1                                            59
Deinococcus radiodurans R1                                           82
Thermotoga maritima MSB8                                             65
Haemophilus influenzae F3031                                        105
Haemophilus influenzae KR494                                        105
Haemophilus aegyptius ATCC 11116                                    105
Haemophilus influenzae 22.4-21                                      105
Haemophilus influenzae PittII                                       105
Haemophilus influenzae PittAA                                       105
Haemophilus influenzae R3021                                        105
Haemophilus influenzae RdAW                                         105
Haemophilus influenzae NT127                                        105
Haemophilus influenzae 7P49H1                                       105
Haemophilus influenzae 10810                                        105
Haemophilus influenzae R2846                                        105
Haemophilus influenzae PittGG                                       105
Haemophilus influenzae PittEE                                       105
Ureaplasma urealyticum serovar 12 str. ATCC 33696                    28
Ureaplasma parvum serovar 1 str. ATCC 27813                          28
Ureaplasma parvum serovar 14 str. ATCC 33697                         28
Chlamydia muridarum Nigg                                             13
Aquifex aeolicus VF5                                                  1
Buchnera aphidicola str. Sg (Schizaphis graminum)                   106
Bacillus cereus VD022                                                66
Bacillus cereus BAG1X2-1                                             66
Bacillus thuringiensis Bt407                                         66
Bacillus thuringiensis serovar kurstaki str. HD73                    66
Bacillus thuringiensis MC28                                          66
Bacillus thuringiensis HD-789                                        66
Bacillus thuringiensis serovar pakistani str. T13001                 66
Bacillus cereus AH676                                                66
Bacillus cereus Rock3-29                                             66
Bacillus cereus Rock3-28                                             66
Bacillus cereus m1550                                                66
Bacillus cereus MM3                                                  66
Brucella abortus 65/63                                               42
Brucella melitensis 11-1823-3434                                     42
Brucella abortus 99-9971-135                                         42
Brucella abortus 07-0994-2411                                        42
Brucella sp. NF 2653                                                 42
Brucella sp. BO1                                                     42
Brucella sp. BO2                                                     42
Brucella suis VBI22                                                  42
Xylella fastidiosa 9a5c                                              83
Thermoanaerobacter tengcongensis MB4                                 84
Vibrio cholerae HC-52A1                                              92
Vibrio cholerae PS15                                                 92
Vibrio cholerae HE-09                                                92
Vibrio cholerae 12129(1)                                             92
Vibrio cholerae O395                                                 92
Chlamydia trachomatis L2b/Ams5                                       14
Chlamydia trachomatis A/363                                          14
Xylella fastidiosa EB92.1                                            85
Xylella fastidiosa Ann-1                                             85
Enterococcus faecalis EnGen0286                                      67
Enterococcus faecalis EnGen0111                                      67
Enterococcus faecalis str. Symbioflor 1                              67
Chlamydophila caviae GPIC                                            15
Shewanella oneidensis MR-1                                           93
Pseudomonas sp. TJI-51                                               94
Pseudomonas putida BIRD-1                                            94
Mycobacterium avium subsp. paratuberculosis MAP4                     21
Pseudomonas aeruginosa DHS29                                        107
Pseudomonas aeruginosa BL09                                         107
Pseudomonas aeruginosa 19660                                        107
Pseudomonas aeruginosa BL06                                         107
Pseudomonas aeruginosa BWHPSA001                                    107
Pseudomonas aeruginosa BWHPSA010                                    107
Pseudomonas aeruginosa BL18                                         107
Pseudomonas aeruginosa BL04                                         107
Pseudomonas aeruginosa E2                                           107
Pseudomonas aeruginosa M9A.1                                        107
Pseudomonas aeruginosa X24509                                       107
Pseudomonas aeruginosa BL14                                         107
Pseudomonas aeruginosa PA7                                          107
Rickettsia sibirica 246                                             108
Rickettsia conorii str. Malish 7                                    108
Rickettsia slovaca str. D-CWPP                                      109
Rickettsia parkeri str. Portsmouth                                  108
Rickettsia africae ESF-5                                            108
Staphylococcus epidermidis IS-K                                      43
Staphylococcus epidermidis VCU144                                    43
Bifidobacterium longum subsp. longum 44B                             68
Bifidobacterium longum subsp. longum 2-2B                            68
Bifidobacterium longum subsp. longum JCM 1217                        68
Haemophilus ducreyi 35000HP                                         110
Agrobacterium fabrum str. C58                                        33
Agrobacterium tumefaciens CCNWGS0286                                 34
Agrobacterium sp. ATCC 31749                                         33
Caulobacter crescentus NA1000                                        29
Bacteroides sp. 1_1_6                                                95
Bacteroides thetaiotaomicron VPI-5482                                95
Lactobacillus johnsonii ATCC 33200                                   35
Lactobacillus johnsonii FI9785                                       35
Lactobacillus johnsonii NCC 533                                      35
Clostridium acetobutylicum ATCC 824                                  44
Pseudomonas syringae pv. lachrymans str. M302278                     96
Pseudomonas syringae pv. morsprunorum str. M302280                   96
Pseudomonas syringae pv. actinidiae str. M302091                     97
Pseudomonas syringae pv. tomato str. DC3000                          96
Bacillus subtilis subsp. subtilis str. 168                           45
Buchnera aphidicola str. JF99 (Acyrthosiphon pisum)                 111
Buchnera aphidicola str. LL01 (Acyrthosiphon pisum)                 111
Buchnera aphidicola str. APS (Acyrthosiphon pisum)                  111
Mycoplasma penetrans HF-2                                            30
Wigglesworthia glossinidia endosymbiont of Glossina brevipalpis      86
Nostoc sp. PCC 7120                                                   5
Anabaena variabilis ATCC 29413                                        6
Onion yellows phytoplasma OY-M                                       69
Corynebacterium efficiens YS-314                                     22
Sinorhizobium meliloti AK83                                          36
Sinorhizobium meliloti BL225C                                        36
Sinorhizobium meliloti GR4                                           36
Sinorhizobium meliloti 2011                                          36
Sinorhizobium medicae WSM419                                         37
Sinorhizobium meliloti SM11                                          36
Oceanobacillus iheyensis HTE831                                      70
Mesorhizobium loti MAFF303099                                        46
Campylobacter jejuni subsp. jejuni PT14                              71
Campylobacter jejuni 4031                                            71
Campylobacter jejuni subsp. jejuni NCTC 11168-BN148                  71
Campylobacter coli CVM N29710                                        72
Campylobacter jejuni subsp. jejuni LMG 23211                         71
Campylobacter jejuni subsp. jejuni 1893                              71
Campylobacter jejuni subsp. jejuni 1213                              71
Campylobacter jejuni subsp. jejuni 1997-11                           71
Campylobacter jejuni subsp. jejuni 2008-894                          71
Campylobacter jejuni subsp. jejuni 86605                             71
Campylobacter jejuni subsp. jejuni LMG 23264                         71
Campylobacter jejuni subsp. jejuni LMG 23263                         71
Campylobacter jejuni subsp. jejuni LMG 23216                         71
Campylobacter coli LMG 9860                                          72
Campylobacter coli 317/04                                            71
Campylobacter jejuni subsp. jejuni 1336                              71
Campylobacter jejuni subsp. jejuni S3                                71
Neisseria meningitidis H44/76                                        47
Borrelia burgdorferi ZS7                                             48
Borrelia burgdorferi JD1                                             48
Borrelia sp. SV1                                                     48
Borrelia burgdorferi 29805                                           49
Borrelia burgdorferi WI91-23                                         48
Borrelia burgdorferi 94a                                             48
Borrelia burgdorferi B31                                             50
Coxiella burnetii RSA 331                                            87
Fusobacterium nucleatum CTI-2                                        73
Fusobacterium nucleatum subsp. nucleatum ATCC 23726                  73
Chlorobium tepidum TLS                                               31
Buchnera aphidicola str. Bp (Baizongia pistaciae)                   112
Clostridium tetani E88                                                2
Helicobacter hepaticus ATCC 51449                                    88
Prochlorococcus marinus subsp. marinus str. CCMP1375                  7
Chromobacterium violaceum ATCC 12472                                 51
Geobacter sulfurreducens PCA                                         98
Treponema denticola F0402                                            74
Treponema denticola ATCC 35405                                       74
Wolbachia endosymbiont of Drosophila melanogaster                    99
Thermus thermophilus HB8                                             75
Thermus thermophilus HB27                                            75
Desulfovibrio vulgaris str. Hildenborough                            76
Mycoplasma mobile 163K                                               16
Mycoplasma genitalium M6320                                          12
Mycoplasma genitalium M2321                                          12
Rhodopseudomonas palustris CGA009                                    38
Rhodopseudomonas palustris TIE-1                                     38
Neisseria meningitidis ATCC 13091                                    52
Neisseria meningitidis alpha14                                       52
Neisseria meningitidis alpha153                                      52
Neisseria meningitidis 961-5945                                      52
Neisseria meningitidis 8013                                          52
Mycoplasma pulmonis                                                  18
Mycobacterium leprae                                                 23
Mycoplasma gallisepticum str. F                                      17
Mycoplasma mycoides subsp. mycoides SC str. Gladysdale               24
Ralstonia solanacearum FQY_4                                         77
Ralstonia solanacearum CMR15                                         77
Ralstonia solanacearum GMI1000                                       77
Streptomyces coelicoflavus ZG0656                                    39
Streptomyces coelicolor A3(2)                                        39
Nitrosomonas europaea ATCC 19718                                     40
Corynebacterium diphtheriae VA01                                     25
Corynebacterium diphtheriae PW8                                      25
Corynebacterium diphtheriae CDCE 8392                                25
Corynebacterium diphtheriae BH8                                      25
Corynebacterium diphtheriae INCA 402                                 25
Corynebacterium diphtheriae                                          25
Corynebacterium diphtheriae HC02                                     25
Rhodopirellula baltica SH 1                                          11
Prochlorococcus marinus subsp. pastoris str. CCMP1986                 8
Prochlorococcus marinus str. MIT 9313                                 9
Synechococcus sp. WH 8102                                            10
Wolinella succinogenes                                               89
Photorhabdus luminescens subsp. laumondii TTO1                      100
Candidatus Blochmannia floridanus                                    78
Bdellovibrio bacteriovorus HD100                                    114
Bartonella henselae str. Houston-1                                   53
Bartonella quintana RM-11                                            54
Bartonella quintana str. Toulouse                                    54
Candidatus Protochlamydia amoebophila UWE25                          19
Pectobacterium atrosepticum SCRI1043                                113
Acinetobacter sp. ADP1                                              101
Thermosynechococcus elongatus BP-1                                    3
Bradyrhizobium japonicum USDA 110                                    55
Gloeobacter violaceus PCC 7421                                       26

DECIPHER documentation built on Nov. 17, 2017, 1:01 p.m.