The tips between divergent nodes or fixation mutations on the lineages are each gathered as group.
groupTips(tree, ...)
# S3 method for phyMSAmatched
groupTips(
tree,
similarity = NULL,
simMatrix = NULL,
forbidTrivial = TRUE,
tipnames = TRUE,
...
)
# S3 method for lineagePath
groupTips(tree, tipnames = TRUE, ...)
# S3 method for sitesMinEntropy
groupTips(tree, tipnames = TRUE, ...)
# S3 method for fixationSites
groupTips(tree, tipnames = TRUE, ...)
# S3 method for fixationPath
groupTips(tree, tipnames = TRUE, ...)The return from addMSA, lineagePath,
sitesMinEntropy or other functions.
Other arguments.
This decides how minor SNPs are to remove. If provided as
fraction between 0 and 1, then the minimum number of SNP will be total tips
times similariy. If provided as integer greater than 1, the minimum
number will be similariy. The default similariy is 0.05 for
lineagePath.
Deprecated and will not have effect.
Does not allow trivial trimming.
If return tips as integer or tip names.
groupTips returns grouping of tips.
data(zikv_tree)
data(zikv_align)
tree <- addMSA(zikv_tree, alignment = zikv_align)
groupTips(tree)
#> $`363`
#> [1] "ANK57896" "AMD61711" "AQS26698" "APG56458" "AUI42289" "AMR39834"
#> [7] "AWH65848" "APO08504" "AMX81917" "AVZ47169" "AMX81916" "AMD61710"
#> [13] "AMK49492" "AMX81915" "AOC50652" "APH11611" "BBC70847" "AUF35022"
#> [19] "ATL14618" "AUF35021"
#>
#> $`513`
#> [1] "APG56499" "ASW34302" "AOL02459" "APH11552" "APH11574" "APH11550"
#> [7] "APH11586" "APH11535" "APH11544" "AWK27349" "APH11584" "APH11567"
#> [13] "APH11548" "APH11572" "APH11575" "APH11568" "APH11561" "APH11533"
#> [19] "APH11523" "APH11545" "APH11554" "APH11553" "APH11558" "APH11564"
#> [25] "APH11509" "APH11537" "APH11521" "APH11555" "APH11577" "APH11525"
#> [31] "APH11570" "APH11565" "APH11541" "APH11583" "APH11501" "APH11524"
#> [37] "APH11505" "APH11546" "APH11582" "APH11585" "APH11557" "APH11579"
#> [43] "APH11540" "APH11495" "AOO19565" "APH11511" "APH11547" "APH11542"
#> [49] "APH11563" "APH11504" "APH11587" "APH11569"
#>
#> $`567`
#> [1] "APH11580" "APH11576" "APH11531" "APH11593" "APH11517" "APH11527"
#> [7] "APH11530" "APH11590" "APH11559" "APH11592" "APH11594" "APH11532"
#> [13] "APH11518" "APH11549" "APH11512" "APH11514" "APH11515" "APH11581"
#> [19] "APH11508" "APH11516" "APH11538" "APH11551" "APH11571" "APH11566"
#> [25] "APH11529" "APH11543" "APH11573" "APH11560" "APH11536" "APH11493"
#> [31] "APH11528" "APH11562" "APH11595"
#>
#> $`556`
#> [1] "AVG19202" "APH11539" "APH11534" "APH11500" "APH11502" "APH11503"
#> [7] "APH11578" "APH11499" "APH11498" "APH11506" "APH11507" "APH11497"
#>
#> $`493`
#> [1] "AVV62004" "BAX00477"
#>
#> $`610`
#> [1] "BAV89190" "AOI20067" "AMM43325" "AMM43326" "ANC90425" "AUI42329"
#> [7] "AUI42330" "AMR68932" "ANF16414" "AMT75536" "AMV49165" "AMO03410"
#> [13] "ANA12599" "AMM39806" "AMR39830"
#>
#> $`489`
#> [1] "ANO46307" "AVG19275" "ANN44857" "ANO46306" "ANO46309" "ANO46305"
#> [7] "ANO46303" "ANO46302" "ANO46301" "ARB08102" "AHZ13508" "ANO46304"
#> [13] "ANO46308" "AMD16557"
#>
#> $`402`
#> [1] "ALX35659" "APY24198" "APO36913" "ANQ92019" "AOX49264" "AOX49265"
#>
#> $`400`
#> [1] "APY24199" "AMH87239" "AMA12086" "AMA12085" "AMU04506" "AMA12087"
#> [7] "AMA12084" "AML81028" "AOY08518" "ARB07962" "AOY08538" "AOG18295"
#> [13] "AOY08517" "AOY08541" "AMM39805" "ARX97119" "AMK79468" "AML82110"
#> [19] "AMR39831" "AMX81918" "APY24200" "AOO19564" "AUI42194" "AOG18296"
#> [25] "ATG29267" "AQX32985" "AQZ41948" "AQZ41954" "AOY08533" "ASL68978"
#> [31] "AQZ41953" "AQZ41947" "AVZ25033" "ATG29291" "ATG29301" "ASL68979"
#> [37] "ATG29299" "AQZ41949" "AQZ41950" "AQZ41951" "ATI21641" "ANO46297"
#> [43] "ANO46298" "APO08503" "ANG09399" "ARU07183" "AQZ41956" "ATG29276"
#> [49] "AOW32303" "ATG29292" "ATG29295" "AOY08536" "ASL68974" "AMQ48986"
#> [55] "ATG29315" "ATG29307" "ATG29270" "AOC50654" "AMC13913" "AMC13912"
#> [61] "APO39243" "APO39229" "AQZ41952" "AQZ41955" "ARI68105" "ASU55505"
#> [67] "AQM74762" "AUD54964" "ART29828" "AWF93617" "APC60215" "ATG29306"
#> [73] "ATG29284" "AQM74761" "ATG29287" "ATG29303" "AWF93619" "AWF93618"
#>
#> $`472`
#> [1] "AMK49165" "ARB07976" "APB03018" "AMC13911" "APB03019" "ASU55416"
#> [7] "ANK57897" "AWH65849" "ASU55417" "ANW07476" "AMZ03556"
#>
#> $`628`
#> [1] "ARU07074" "AMX81919" "AMB37295" "ANC90426" "ALU33341"
#> [6] "ASB32509" "ARU07076" "ATB53752" "AOR82893" "ARU07075"
#> [11] "AMQ48982" "AMK49164" "APG56457" "ANH10698" "AOR82892"
#> [16] "AMB18850" "YP_009428568" "ART29823" "ASK51714" "ARB07953"
#> [21] "AOY08537" "AOY08523" "ASW34087" "AOS90224" "BAV82373"
#> [26] "ART29826" "ART29825" "AOY08525" "AOY08535" "APW84875"
#> [31] "APW84874" "APW84873" "APW84876" "ANH22038" "APW84877"
#> [36] "APW84872" "AMN14620" "AVZ25035" "AOY08542" "ARB07932"
#> [41] "AOS90223" "AOS90220" "APO39232" "APO39233" "AOO85388"
#> [46] "AOO53981" "AOS90222" "APO39228" "AOS90221" "AOY08546"
#> [51] "AOY08521" "AOY08516" "APB03021" "APO39236" "APO39237"
#> [56] "APB03020"
#>
#> $`409`
#> [1] "AQU12485" "AMQ48981" "APH11492" "AOO54270" "AND01116" "AMS00611"
#> [7] "ARB07967" "ANF04752" "AOE22997" "ASU55403" "ASU55393" "ANB66184"
#> [13] "AMC33116" "ASU55400" "ASU55409" "AMQ34003" "AMQ34004" "AMM39804"
#> [19] "ASU55411" "ASU55395" "AMZ03557" "APQ41784" "ASU55391" "ASU55396"
#> [25] "ASU55392" "AOY08524" "ASU55394" "APQ41782" "ASU55399" "APQ41783"
#> [31] "ANS60026" "ASU55408" "ANC90428" "ASU55418" "ASU55424" "AQX32987"
#> [37] "APB03017" "ASU55410" "ASU55397" "ASU55413" "ASU55420" "ASU55404"
#> [43] "ASU55423" "ANB66182" "ASU55425" "ASU55406" "ASU55398" "ASU55407"
#> [49] "ASU55414" "ASU55405" "ASU55401" "ASU55402" "ASU55421" "ASU55415"
#> [55] "ASU55426" "ASU55412" "ASU55419" "APQ41786" "ASU55390" "AQX32986"
#> [61] "ASU55422" "ARM59239" "ANB66183"
#>