Package: mdelta
mDELTA: an algorithm formultifuricatingDevelopmental cEllLineageTreeAlignment.mDELTAis an algorithm formultifuricatingDevelopmental
cEllLineageTreeAlignment. In essence, it compares two
rooted, unordered, tip-labeled trees, and finds the best global /
local correspondence between the nodes. ThemDELTAprogram is
designed for analyzing developmental cell lineage trees
reconstructed through single-cell DNA barcoding (such as done by
scGESTALT or SMALT, while greater cellular coverage is expected to
yield more meaningfulmDELTAalignments).Except for dealing with cell lineage trees instead of biological
sequences,mDELTAis conceptually similar to sequence alignment.
It helps quantify similarity among different lineage trees,
disentangle the consensus and variation, find recurrent motifs, and
facilitate comparative/evolutionary analyses.Also included in this repository are Python/R scripts for
statistical analyses and visualization ofmDELTAresults, which
facilitates their biological interpretation.mDELTAwas developed by Jingyu Chen under the supervision of
Professor Jian-Rong Yang at the Zhongshan School of Medicine of Sun
Yat-Sen University in China.For details, please visithttps://github.com/Chenjy0212/mdelta/blob/main/README2.md/Quick startInstallationpipinstallmdeltaThis will installmDELTAand its prerequisitesRunning the programmDELTA.py-husage:mDELTA[-h][-ntNAME2TYPEFILE][-nt2NAME2TYPEFILE2][-sdSCOREDICTFILE][-tTOP][-maMAV][-miMIV][-pPV][-TTQDM][-nNOTEBOOK][-PPERM][-aALG][-cCPUS][-oOUTPUT][-xDIFF][-mgMERGE]TreeSeqFileTreeSeqFile2

MultifuricatingDevelopmentalcEllLineageTreeAlignment(mDELTA)positionalarguments:TreeSeqFile[path/filename]Atextfilestoringcelllineagetree#1 in newick format. Tips can be labeled by name orcelltype.Branchlengthsshouldberemoved.TreeSeqFile2[path/filename]Atextfilestoringcelllineagetree#2 in newick format. Tips can be labeled by name orcelltype.Branchlengthsshouldberemoved.

optionalarguments:-h,--helpshowthishelpmessageandexit-ntNAME2TYPEFILE,--Name2TypeFileNAME2TYPEFILE[path/filename]Listofcorrespondancebetweentipnameandcelltypeforcelllineagetree#1.-nt2NAME2TYPEFILE2,--Name2TypeFile2NAME2TYPEFILE2[path/filename]Listofcorrespondancebetweentipnameandcelltypeforcelllineagetree#2.-sdSCOREDICTFILE,--ScoreDictFileSCOREDICTFILE[path/filename]Acomma-delimitedtextfileusedtodeterminesimilarityscoresbetweencells.Ifthereareexactlythreecolumns,theywillbeinterpretedas(1)thecell(nameortype)inTree#1, (2) thecellinTree#2, and (3) the similarity score. If otherwise, the first column will be interpreted as thecell(nameortype)andtheremainingcolumnsasfeaturesofthecell(e.g.expressionofagene).ThesimilarityscoreswillbeestimatedbetweenallpairsofcellsbasedontheEuclideandistancecalculatedusingallthefeatures.Overrides`-ma`and`-mi`.-tTOPN,--topTOPN[int>0]Performslocal(insteadofglobal)alignment,andoutputthetopTOPNUMlocalalignmentswiththehighestscore(e.g.`-t10`).Inthecaseofglobalalignment,thisparametershouldbeomitted.-maMAV,--mavMAV[float]-miMIV,--mivMIV[float]Shorthandforasimplematchingscorescheme,wherethematchingscorebetweenapairofthesamecelltypesisMAVandallotherpairsareMIV.(e.g.`-ma2-mi-2`).Overriddenby`-sd`.-pPV,--pvPV[float]Thescoreforpruningatipofthetree(e.g.`-p-2`).Defaultto-1.-TTQDM,--TqdmTQDM[0(off)or1(on)]Toggleforthejupyternotebookenvironment.-nNOTEBOOK,--notebookNOTEBOOK[0(off)or1(on)]Toggleforthejupyternotebookenvironment.-PPERM,--PERMPERM[int>0]Toggleforthestatisticalsignificance.Foreachobservedalignment,thealignedtreeswillbepermutedPERMtimestogenerateanulldistributionofalignmentscores,withwhichaPvaluecanbecalculatedfortheobservedalignmentscore.-aALG,--AlgALG[KM/GA]UseKuhn-MunkresorGreedyAlgorithmtofindtheoptimalalignmentscore.-cCPUS,--CPUsCPUS[int>0]Numberofthreadsformulti-processing.Defaultto50.,itcanreachthemaximumnumberoflocalCPUcores-1.-oOUTPUT,--outputOUTPUT[path/filename]Outputfilename-xDIFF,--diffDIFF[int>0]AlignmentmustconsistofaminimalofDIFF%alignedcellpairsthataredifferentfromprevious(better)localalignmentsinordertobeconsideredasanothernewalignment(e.g.`-x20`means20%).-mgMERGE,--mergeMERGE[float]Thisisthescalingfactorforcalculatingthescoreofmerginganinternalnode(e.g.-mg-1),whichismultipliedbythenumberoftipsoftheinternalnodetobemerged.Defaultto0.

Moredetailsonhttps://github.com/Chenjy0212/mdeltaAligning a tree with itself, output top three local alignmentsmDELTA.pyExampleFile/tree.nwkExampleFile/tree.nwk-t3:writing_hand: AuthorsJingyu Chen (EeWhile) :man:Student ofSYSU. :school:ZHONGSHAN SCHOOL OF MEDICINE,SYSUhttps://zssom.sysu.edu.cn/zh-hans:sparkling_heart:Undergraduate majoring in computer science, master majoring in
bioinformatics. :man_technologist:Below is the contact information of the author. :eyes:If you use this project in your research, please cite this project.@misc{mdelta2022,
    author ={Jingyu Chen},
    title ={mDELTA: Multifuricating Developmental cEll Lineage Tree Alignment},
    year ={2022},
    publisher ={GitHub},
    journal ={GitHub repository},
    howpublished ={\url{https://github.com/Chenjy0212/mdelta}},}