In viral evolution, fixed substitutions in the nucleic acid or protein level are closely associated with maintaining viral function, while parallel mutation reflects the competitive nature in adaptive selection. The continued accumulation of large-scale viral sequence data enhances the challenge of identifying important mutations in a quick and accurate manner. In sitePath, the phylogenetic tree was separated into a set of inheritable phylogenetic pathways via an automated pathway-division method. Then, for each phylogenetic pathway, the identification of fixed substitutions was transformed into a local-optimal-solution problem directed by a minimal entropy algorithm. Finally, the parallel mutation was determined based on the recurrence of mutations among at least two phylogenetic pathways.
sitePath 1.20.0
The sitePath
package is made for the high-throughput identification of fixed substitutions and parallel mutations in viruses from a single phylogenetic tree. This is achieved by three major steps:
The firs step is to import phylogenetic tree and multiple sequence alignment files. For now, sitePath
accepts phylo
object and alignment
object. Functions from ggtree
and seqinr
are able to handle most file formats.
The S3 phylo
class is a common data structure for phylogenetic analysis in R. The CRAN package ape provides basic parsing function for reading tree files. The Bioconductor package treeio provides more comprehensive parsing utilities.
library(sitePath)
tree_file <- system.file("extdata", "ZIKV.newick", package = "sitePath")
tree <- read.tree(tree_file)
It is highly recommended that the file stores a rooted tree as R would consider the tree is rooted by default and re-rooting the tree in R is difficult. Also, we expect the tree to have no super long branches. A bad example is shown below:
Most multiple sequence alignment format can be parsed by seqinr. There is a wrapper function for parsing and adding the sequence alignment. Set “cl.cores” in options
to the number of cores you want to use for multiprocessing.
alignment_file <- system.file("extdata", "ZIKV.fasta", package = "sitePath")
options(list("cl.cores" = 1)) # Set this bigger than 1 to use multiprocessing
paths <- addMSA(tree, msaPath = alignment_file, msaFormat = "fasta")
The addMSA
function will match the sequence names in tree and alignment. Also, the function uses polymorphism of each site to cluster sequences for identifying phylogenetic pathways.
After importing the tree and sequence file, sitePath
is ready to identify phylogenetic pathways.
The impact of threshold depends on the tree topology hence there is no universal choice. The function sneakPeak
samples thresholds and calculates the resulting number of paths. The use of this function can help choose the threshold.
preassessment <- sneakPeek(paths, makePlot = TRUE)
The default threshold is the first ‘stable’ value to produce the same number of phylogenetic pathways. You can directly use the return of addMSA
if you want the default or choose other threshold by using function lineagePath
. The choice of the threshold really depends. Here 18 is used as an example.
paths <- lineagePath(preassessment, 18)
paths
#> This is a 'lineagePath' object.
#>
#> 4 lineage paths using 18 as "major SNP" threshold
You can visualize the result.
plot(paths)
Now you’re ready to find fixation and parallel mutations.
The sitesMinEntropy
function perform entropy minimization on every site for each lineage. The fixation and parallel mutations can be derived from the function’s return value.
minEntropy <- sitesMinEntropy(paths)
The hierarchical search is done by fixationSites
function. The function detects the site with fixation mutation.
fixations <- fixationSites(minEntropy)
fixations
#> This is a 'fixationSites' object.
#>
#> Result for 4 paths:
#>
#> 139 894 2074 2086 2634 3045 988 1143 2842 3398 107 1118 3353
#> No reference sequence specified. Using alignment numbering
To get the position of all the resulting sites, allSitesName
can be used on the return of fixationSites
and also other functions like SNPsites
and parallelSites
.
allSites <- allSitesName(fixations)
allSites
#> [1] "139" "894" "2074" "2086" "2634" "3045" "988" "1143" "2842" "3398"
#> [11] "107" "1118" "3353"
If you want to retrieve the result of a single site, you can pass the result of fixationSites
and the site index to extractSite
function. The output is a sitePath
object which stores the tip names.
sp <- extractSite(fixations, 139)
It is also possible to retrieve the tips involved in the fixation of the site.
extractTips(fixations, 139)
#> [[1]]
#> [1] "ANK57896" "AMD61711" "AQS26698" "APG56458" "AUI42289" "AMR39834"
#> [7] "AWH65848" "APO08504" "AMX81917" "AVZ47169" "AMX81916" "AMD61710"
#> [13] "AMK49492" "AMX81915" "AOC50652" "APH11611" "BBC70847" "AUF35022"
#> [19] "ATL14618" "AUF35021" "AVV62004" "BAX00477"
#> attr(,"AA")
#> [1] "S"
#>
#> [[2]]
#> [1] "BAV89190" "AOI20067" "AMM43325" "AMM43326" "AUI42329"
#> [6] "AUI42330" "ANC90425" "AMT75536" "ANF16414" "AMR68932"
#> [11] "ANA12599" "AMM39806" "AMR39830" "AMV49165" "AMO03410"
#> [16] "ANO46307" "AVG19275" "ANN44857" "ANO46306" "ANO46309"
#> [21] "ANO46305" "ANO46303" "ARB08102" "ANO46302" "AHZ13508"
#> [26] "ANO46304" "ANO46301" "ANO46308" "AOG18296" "AOO19564"
#> [31] "AUI42194" "APC60215" "AMQ48986" "ATG29307" "ART29828"
#> [36] "AWF93617" "ATG29284" "ATG29287" "ATG29303" "AWF93619"
#> [41] "AWF93618" "AQM74762" "AUD54964" "AQM74761" "ATG29306"
#> [46] "ASL68974" "ATG29267" "ASL68978" "AQX32985" "ATG29315"
#> [51] "AQZ41956" "ARI68105" "ASU55505" "AQZ41949" "ASL68979"
#> [56] "ATG29299" "ATI21641" "ATG29270" "ATG29291" "AOY08536"
#> [61] "ANO46297" "ANO46298" "AQZ41950" "AQZ41951" "ARU07183"
#> [66] "ANG09399" "AQZ41954" "AOY08533" "AQZ41947" "AQZ41948"
#> [71] "ATG29292" "ATG29295" "AOW32303" "AVZ25033" "AOC50654"
#> [76] "AQZ41953" "ATG29301" "ATG29276" "APO08503" "AMC13913"
#> [81] "AMC13912" "APO39243" "APO39229" "AQZ41952" "AQZ41955"
#> [86] "AMK49165" "ARB07976" "APB03018" "AMC13911" "APB03019"
#> [91] "ASU55416" "ANK57897" "AWH65849" "AMZ03556" "ASU55417"
#> [96] "ANW07476" "APY24199" "AMA12086" "AMH87239" "APY24198"
#> [101] "APO36913" "ALX35659" "AOG18295" "ANQ92019" "AML81028"
#> [106] "APY24200" "AMD16557" "ARU07074" "AOX49264" "AOX49265"
#> [111] "AOY08518" "ARB07962" "AMX81919" "AMM39805" "ARX97119"
#> [116] "AMB37295" "AMK79468" "AML82110" "AMR39831" "AMX81918"
#> [121] "ANC90426" "ALU33341" "ASB32509" "AMA12085" "AMU04506"
#> [126] "AMA12087" "AMA12084" "AQU12485" "AMS00611" "AMQ48981"
#> [131] "AOY08538" "APH11492" "AOY08517" "AOY08541" "AOO54270"
#> [136] "AND01116" "ARU07076" "AMK49164" "APG56457" "AOR82892"
#> [141] "ATB53752" "ANH10698" "AOR82893" "ARU07075" "AMB18850"
#> [146] "YP_009428568" "AMQ48982" "ART29823" "APW84876" "ASK51714"
#> [151] "ARB07953" "APW84872" "AOY08525" "APW84873" "AOY08535"
#> [156] "AVZ25035" "ARB07932" "AOY08523" "AOY08542" "ASW34087"
#> [161] "AOY08537" "APB03020" "ART29826" "ART29825" "AOS90220"
#> [166] "AMN14620" "APW84874" "APW84875" "BAV82373" "AOS90221"
#> [171] "AOS90224" "APB03021" "APO39232" "AOS90223" "APO39237"
#> [176] "ANH22038" "APW84877" "APO39236" "AOY08546" "AOY08516"
#> [181] "APO39233" "AOS90222" "AOO53981" "AOY08521" "AOO85388"
#> [186] "APO39228" "ARB07967" "ANF04752" "AOE22997" "APQ41782"
#> [191] "APQ41786" "ASU55393" "ASU55404" "ASU55423" "ANB66182"
#> [196] "ASU55425" "ASU55420" "AQX32986" "ASU55422" "APQ41784"
#> [201] "ANC90428" "ASU55415" "ASU55418" "ARM59239" "ASU55408"
#> [206] "ASU55424" "ASU55390" "ASU55419" "ASU55391" "AMM39804"
#> [211] "ASU55411" "ANB66183" "ASU55421" "AMZ03557" "ASU55392"
#> [216] "AQX32987" "ASU55403" "ASU55399" "APQ41783" "ANS60026"
#> [221] "ANB66184" "ASU55426" "ASU55412" "ASU55413" "ASU55410"
#> [226] "ASU55397" "ASU55400" "ASU55409" "APB03017" "ASU55395"
#> [231] "ASU55396" "AOY08524" "ASU55394" "ASU55414" "ASU55405"
#> [236] "AMC33116" "ASU55406" "ASU55398" "ASU55407" "AMQ34003"
#> [241] "AMQ34004" "ASU55401" "ASU55402"
#> attr(,"AA")
#> [1] "N"
Use plot
on a sitePath
object to visualize the fixation mutation of a single site. Alternatively, use plotSingleSite
on an fixationSites
object with the site specified.
plot(sp)
plotSingleSite(fixations, 139)
To have an overall view of the transition of fixation mutation:
plot(fixations)
Parallel mutation can be found by the parallelSites
function. There are four ways of defining the parallel mutation: all
, exact
, pre
and post
. Here exact
is used as an example.
paraSites <- parallelSites(minEntropy, minSNP = 1, mutMode = "exact")
paraSites
#> This is a 'parallelSites' object.
#>
#> Result for 4 paths:
#>
#> 105 1264 1226 1717 988 2611 2787 2749 3328 3162 1857 3046 1016 1171 1327 3076 106 2357 573 1404 940 1180
#> No reference sequence specified. Using alignment numbering
The result of a single site can be visualized by plotSingleSite
function.
plotSingleSite(paraSites, 105)
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
#> ! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
To have an overall view of the parallel mutations:
plot(paraSites)