PhyloType User Manual V1.4
Contents
1. Figure 1 Overview of the PhyloType pipeline and screenshot of its Web interface A Phylotype analysis is composed of five sequential steps Input Tree Annotation Analysis and Output The Web interface organizes these steps as a notebook in which each tab corresponds to a given step indicated by the red arrows To validate a given step submitting data combining annotations launching an analysis etc and to move forward the next step you must click the arrow button and select the corresponding tab manually Moreover a given step may have internal operations such as rooting the tree within the Tree step or combining annotations within the Annotation step To run this kind of operation click on the Go button PhyloType User Manual v1 4 Page 2 2 The Input step A tree and its annotations are submitted by Copy Paste or by Upload Trees to be analyzed must be in Newick format Trees must be rooted with care and must contain branch lengths Trees can contain support values such as bootstrap posterior probabilities and likelihood ratio Supports Example B_86DEHAN 0 018569 CBW3871 In this example the Newick string contains support values 3 0 012185 50 0 002353 CBW9606M and branch lengths Support values are in front of the JAS6MOLE 1chi 0 026038 40 0 00673 character and branch lengths are after the character 8 5 When submitting data using Copy Paste don t forget to include the character2. gt es n as gt a ini o eA Tats 7 7 4 AU SANAN ANAN Ka f vata EANA 446 UUU Z U 2 30 l UUU 16 000 U UUS tA 0 172 0 051 0 051 1 000 1 UUU hylolType analysis A01 Criteria ACCTRAN Sz 5 Ps 1 SzDf 1 Sp 8 Sz p va eshold 5 1000 gt phylotype s related to 4 annotation spg Figure 6 Screenshot of the Overview table in the Analysis step This table lists annotations for which phylotypes have been found and the mean values for each criterion The first row of the table contains a reminder of PhyloType parameterization 1 and if a shuffling process has been used a menu to select phylotypes given a p value threshold for the Sz criterion 2 In this example the analysis was called A01 4 phylotypes were found covering 71 of tips of the tree and corresponding to 4 different annotations These 4 phylotypes are supported with a p value lt 0 05 for the Sz criterion The first column of the table named A displays the annotations associated with the phylotypes found by the analysis 3 The second column P contains the number of phylotypes associated with each annotation The third criteria Cov Coverage displays the percentage of taxa annotated with the corresponding annotation and phylotype s In this example 88 of the Africa sequences in the tree belong to only one phylotype The following columns display mean values for each criterion Criteria with an orange background are the
3. last column AnB Ancestor Break displays ancestral annotations between the phylotype and its ancestor if one exists if these annotations are different from those of the ancestor and the phylotype The table can be ordered by clicking on column titles first row of the table Input Tree Annotation Analysis Output PhyloType analysis A01 ACCTRAN Sz 5 Ps 1 SzDf 1 Sp 0 7 Shuffling 1000 Szp valuetreshold 5 1000 a Display list v total of 4 phylotype s related to 4 annotation s involving 109 strains 71 2 download map tree Click on the variable name to sort values in the table annotations a Sion a a a aa oncestralannotations Fan w r pe 52 16 0 009 0009 0 172 0 051 0 051 1 000 1 000 O0GA4 0 1000 sso 1000 194 4000 G 1 6 000 z gt i x a 1 0 057 0 065 0 035 B46 885 000 00 0 1000 1 1000 0 1000 0 057 0 065 0 035 1646 1 886 1 000 1 27 2 13 500 0 880 0 88 A 0 7000 473 140 wee oP S A ts ee 2 i 15 0 960 IALA 0 4000 7 4000 2 1000 H Figure 7 Screenshot of the Output step the detailed list of phylotypes PhyloType User Manual v1 4 Page 14 6 2 Phylotype map The phylotype map is a tree like view of phylotypes Phylotypes are organized with respect to tree topology with their hierarchical relationships The map display is split into two parts The left part is a global view of the map Figure 8a 1 and the right part is a zoom in view of the map Figur
4. C Global Support SpG ba lteration total 10002 34587 Size Sz Persistence Ps and Size Different Sz Df are mandatory criteria We recommend to not relax default thresholds 5 1 and 1 respectively otherwise meaningless phylotypes may result If supporvalues are available we strongly recommend using Support Sp Shuffling typically 1000 iterations and low p values e g 1 are strongly recommended eT Name Of analysis at 8 I Shuffling P values Ancestral Annotations Nference ACCTRAN Number of iterations j ooo 1 cluding Outgrou p m Overview of the PhyloType analysis A01 Criteria ACCTRAN Sz 5 Ps 1H SDf 1 Sp 0 7 Sz p value treshold 1000 1000 gt total of 4 phylotype s related to 4 annotation s involving 109 strains 71 2 i A P rey 4 Africa 1 88 44 000 2 0 2 750 152 000 16 000 0 009 0009 o172 0051 0 051 1 000 1 000 Albania 1 97 30 000 30 30 000 32 000 1 00 o17 0 059 0024 omis 2415 0960 0 960 EastEuroj 1 80 8 000 10 8 000 9 000 1000 0057 0065 0 035 1646 1886 1 000 1 000 Greece 1 69 27 000 20 13 500 60 000 2 000 0 009 0 073 0 066 0132 1 097 osso oss0 Figure 5 Screenshot of PhyloType Web interface the Analysis step The Web interface of the Analysis step is composed of five panels The first panel 1 deals with the selection of criteria and their parameterization The criteria Sz Ps an
5. Primary annotations panel corresponds to the annotations submitted during the nput step It displays each annotation variable with its domain of values The added New annotations panel displays annotations that will be defined here The controls available for building new annotations are described in Table 1 LIRMM MAB BIOAFRICA w1 0 Jun 2040 PhyloType Home Interface User Guide Annotation Analysis Defining new annotations to be explored optional select and combine annotations to define the annotations to be used by PhyloType Primary annotations New annotations Country E demo 0 0 Albania 31 17 4 Belgium 1 0 6 BieloRussia 1 0 6 Cameroon 6 3 4 Cyprus 23 12 9 Czech 5 2 8 Denmak 1 0 6 DAC 2 1 1 France 3 1 75 Gabon 2 1 1 Greece 40 22 55 oft a if delete variable demo Ki c add value s selection from one variable only to demo g add remaining value s from demo to demo amp tf add value s with a OR connector selection from one variable only to demo name Afita E e add value s with an AND connector multiple variables selection to demo gt oe f rename value s primary annotations cannot be modified with name I ia remove value s primary annotations cannot be modified 4 Current list of annotation variables Variable History demo New Country pri
6. on the Go button Figure 11 4 and wait until the zip file is available to download Figure 11 5 PhyloType fome lrtertece Weer Goede Suppo mentary Materia Toots OTEN Fros Output Phyo T yoo anolyels ADT AC RAN Sz Shi s sri Src shuMmg 1G Scpswue Pesholgs 5 1000 _ Display fist o total ef 4 Dtnionois tate io 4 3 Hwohng 109 strains 17125 Phx Tree amp Phytotppes Tree amp PHyotypes Prylocypes m rectengey me foreground recat p n aed barigrmung Meo pew ard ren b a 2 voor fat SVG Pr MT SVG oy Tree amp Pnytotypes Tree amp Peytotypes Tree amp Ancestral i Tree amp Aroni secs atxi trregecord canta ard backgroud Annetatioos tctanguie Annotations coe Gl eel Sve Pol Pet ave ial PS GvG Gl fel Sve 1 0 Mo 5 iy Cav Iv esy Maa Figure 11 Screenshot of the Output step downloading PhyloType output PhyloType User Manual v1 4 Page 19
7. required criteria Sz Ps and Sz Df 4 The criteria with a green background are the additional criteria selected by the user for phylotype identification in this example So was used as an additional criteria 5 The other criteria grey background are calculated by PhyloType but are not used for identifying phylotypes By clicking on the column s name first row the user can sort values by alphabetical order annotation as shown in this example with light green background or by increasing decreasing values criteria Click on the arrow button to access the detailed results of the analysis the Output step 6 PhyloType User Manual v1 4 Page 12 Table 2 The criteria for the identification of PhyloType Sz 2 size number of strains in the phylotype only strains with studied annotations are counted and considered as belonging to the phylotype see article for formal definition Ps z persistence number of generations with studied annotations starting from the phylotype root Sz Df Z ratio of size Sz and eee Df Semedeteomoge O associated to the phylotype Te Silane see article for formal definition Fer local separation local separation length of the branch from which the phylotype stems of the branch from which the phylotype stems global separation value of a weighted combination of local separation starting from the phylotype root and considering all its ascendants all the way to the tree r
8. the phylotype lists For instance Figure 8b displays a red phylotype 789 EasternEurope which has a phylotype ancestor 1 CentralAfrica The break in ancestral annotation means that there are one or more nodes between the two roots of these phylotypes that are not annotated neither CentralAfrica nor EasternEurope The phylotype map legend indicates that this break is due to one or more nodes being annotated as SouthernAfrica E Southernstrica a SouthAfrica Gp SouthAficalSouthemAfricapSouthemAtrica ED NorthemEurope ED NorthemEurope l D 077 CentralAmerica Figure 8b Screenshot of the Output step the phylotype map PhyloType User Manual v1 4 Page 16 6 3 Tree with color coded phylotypes The phylogenetic tree is displayed with color encoded phylotypes for a given Sz p value threshold Figure 9 1 The color palette for phylotypes is the same as that used for the phylotype map The display is split into two parts The left part is a global view of the map Figure 9 2 and the right part is a zoom in view of the map Figure 9 3 Move the blue rectangle Figure 9 4 from the global view to navigate the tree and update the local view Resize the blue rectangle by grabbing the bottom right corner to modify the zoom ratio Each phylotype is annotated the identifier of its associated node Knowing this node s identifier you can access the information related to the phylotype Figure 8 5 Different kinds of phylotype color co
9. 1000 1000 Gs Display ancestralannotations gt total of 18 phylotype s related to 12 annotation s involving 104 strains 68 0 2 download i i i i 1 Wi A NA EN l Vi i I i e A eager Pui T r T Figure 11 Screenshot of the Output step the tree with color coded ancestral annotations PhyloType User Manual v1 4 Page 18 7 Downloading PhyloType output To download PhyloType output click the arrow button top right of Output Figure 11 1 Make sure you have selected the correct Sz p value threshold Figure 11 2 All PhyloType outputs are listed here You must select one or several file formats if available Figure 11 3 e JPG a bitmap output e PS PostScript vector output for a high quality graphic image May be viewed with GSview a graphical interface for Ghostscript an interpreter for the PostScript page description language used by laser printers e SVG the W3C standard Scalable Vector Graphics SVG file format high quality graphics You can use the free Inkscape vector graphics editor a powerful and convenient drawing tool that is fully compliant with XML SVG and CSS standards Annotations are available in CSV format The file integrates the primary annotations but also any new annotations built in the Annotation step This format saves the table s column layout for use with nearly any spreadsheet application After selecting the files click
10. OUA UNBE PhyloType User Manual v1 4 Overview The nput step The Tree step The Annotation step The Analysis step The Output step Downloading PhyloType output PhyloType User Manual vi francois chevenet ird fr www phylotype org http nwa ptytetype T www phylotype ong PietoTwpe uses a rooted piniopety Of Sane and enn talons assotived M Tage Stara E ules Parheneny 1o inier anceasre annoahens and combinatorial statistic al crteria for the identication ot pryletypes Cambimatorial tiitena eesure Pal a phylo pe Comains enough srans wih a same awotwion as he subtree root ard halil does not contens too many diferent internal sub clusters Statistical cena combine genetic Mormogenety and sepaewion Phplotype is a fee Simpie Use Web savice dedicated te analysing pliylogene tc and amataina elaboneteps you use Gwe siie please cite PryloType Combing annotations and phrylopenies appkeation to wruses Chevenst F Jung N Angon Chfofeau AN Lalor V Letrveasiaiea H de Oliveira T Gastuei O Submited Contaci Finding LiSA LN Fran ois Chavanat Tulo da Olvera Ohver Gasctuel hancots chevenetiPird t tieclveiragPalticacenteacza gascuei innir Screenshot of the PhyloType Web interface www phylotype org please contact the authors by e mail for details or technical problems francois chevenet lirmm fr POPETI DE nnne A T POODE VAD ae A E Tree with color coded phylotypeS eeesssesssesseserressrrssrresrressrrrsrrrssrens
11. ariatieo p108 41 4 furs Tet 7 4 r cf nI x 2j meate a new vanable wih the name 24s gupicate variable Vanstied tol re s07 F galete vananie Vanatie l u FC add vatuets setection tram ana variasie ontyjte Vananen C add remaining vatssis rom Vanazien v to Vanatiedt uF adgvatuets with 2 OR connecter zeiechon Hom ene varaaie oniy to Vanabled tae name fins n A A SN M SAD ESA ADS CIAN SB IT N C remoro values pnmary annotations cannat be modfed Pramary annololiets New annotations coptonent Lountry Vaitabie t a F 37 Aten ft Ala sj C anaie anew variable wit the nama s4077 quphcate varabie Vanatie tolaccsom w C delete variablo Vanabied1 F ada walumin Beiecton from on variatie onty te Vanariaot t fe remaining vatue s trom Couzy af to Vanat y NARA igion tom one xaiye orty to Varabird name C adt values with an AND connecter mettipte variables se echon to Varabied C remane yaueia priman senotatons cannot oe moded win name w T remo value s primary annotations cannet ce moafied PhyloType User Manual v1 4 For each variable PhyloType displays the frequencies of each value For instance the Continent variable has five values the first one being Africa with a frequency of 108 41 4 of the sequences in the tree have this annotation Click to select create a new variable enter th
12. at the end of the Newick string Annotation format Annotations are in CSV format Comma Separated Values The first row contains names of annotation variables All variable names are separated by comma with a space character before and after the comma Names of variables cannot contain specific characters space comma brackets etc The first variable first column corresponds to the tip labels from the tree Note that tip labels are case sensitive They must be exactly the same as in the Newick string Second and following rows of the annotation file contain values for the variables described in the first row Each value is quoted and monovalued no space character Values of a given record a row are separated by a comma with or without space character before and or after it A star character is used for unknown values PhyloType manages missing data for annotations Example Sequence Country In this example the first row saves the name of two variables B_86DEHAN US Sequence and Country The first one Sequence is related B_89SP061 US to the names of the tips in the tree case sensitive The second A2_97CD_KFE4 DRC column Country is an annotation variable it saves the A2_97CD_KTB48 DRC country for each tip For instance the first row A_96CM_MP512 Cameroon B_ 86DEHAN US indicates the Country US for the Sequence B_86DEHAN a tip in the tree Co
13. d Sz Df foreground color orange are always required By default their thresholds are 2 1 and 2 respectively In this example Sp is selected as an additional criterion with a threshold value of 0 7 The second panel is used for the selection of annotations 2 selection of a variable Country in this example and selection of one or several annotation s to study or all as in this example A third panel blue background integrates an entry for naming the analysis a01 in this example 3 switching on off the shuffling process with its number of iterations 4 and choosing the method for the inference of ancestral annotations ACCTRAN or DELTRAN with or without taking into account the tree outgroup The process is activated by clicking on Go The corresponding analysis is computed in a few seconds and if the shuffling process is activated each iterative step is displayed during the computation 6 Lastly a table is returned at the bottom of the window with an overview of the results 7 All analyses are saved by PhyloType User Manual v1 4 Page 11 PhyloType You can go back to an overview table of a given analysis without rerunning the computation To do this simply select the analysis you want to visualize 8 and click on the Display button To access the detailed results of an analysis press the arrow 9 and select the Output tab Overview o 0 7 total of 4 s involving 109 strains 71 2 C Cov l
14. ding background or foreground and different kinds of tree shapes are available Figure 8 6 A red dot posted on an internal edge of the tree indicates a non unique ancestral annotation PhyloType analysis A01 DELTRAN Sz 2 Ps 1 SzDf 2 Sp 0 7 Shuffling 100 Szp valuetreshold lt 5 100 Display tree total of 13 phylotype s related to 11 annotation s among 82 strains 46 1 3 iiia AIL IRENI Phylotyaas 160 7 A 99BED99 At OOKE KNH1207 977202 A1 00KE MSAL076 z z Al OOKE KER2009 n H12 z AT_OOKE_KNH1144 erm AY OKE KER S20 22000 Al 98UG 57142 T 16 A1 KE KSM4021 At OOKE MSA4069 A1 OOKE KNHT209 si 0 0030 GRB2947785 z als A1 OOKE KNH1199 rng N Dy 0 0691 Al 0OKE KSM40 0435 At RW 024 a_i g Dv 0 1975 Sp 0 7650 S A1 OOKE_KE Q color coded background full window foreground s backgroundcircular foregroundcircular Figure 9 Screenshot of the Output step the tree with color coded phylotypes PhyloType User Manual v1 4 Page 17 6 4 Tree with color coded ancestral annotations The phylogenetic tree is displayed with color coded ancestral annotations Figure 11 Non unique ancestral annotations are represented with a unique identifier corresponding to a given combination of annotations input Tree Annotation Analysis Output PhyloType analysis ANALYSIS ACCTRAN Sz 2 Ps 1 SzDf 1 Sp 0 7 Shuffling 1000 Sz p value treshold lt
15. e 8a 2 Move the blue rectangle Figure 8a 3 from the global view to navigate around the map and update the local view Resize the blue rectangle by grabbing the bottom right corner to modify the zoom ratio Each phylotype is represented by a circle with a size proportional to its Sz value Each phylotype is annotated with its annotation and the identifier of the node Knowing this node s identifier you can access all the information related to the phylotype Figure 8a 4 PhyloType analysis A01 DELTRAN Sz 2 Ps 1 SzDf 2 Sp 0 7 Shuffling 100 Sz p value treshold 5 100 Display map total of 13 phylotype s related to 11 annotation s among 82 strains 46 1 _ t 1US downlo 137 Uganda 299 Albania a 326 Albania i RP N 202 Greece Dv 0 0490 252 Cyprus be i SVDv 0 1304 Sa Dv 1 1296 346 Cyprus Sp 0 7690 8 S GR15787404 33 Czech 63 Cameroon 80 Senegal full window Figure 8a Screenshot of the Output step the phylotype map PhyloType User Manual v1 4 Page 15 The phylotype map may include phylotypes with a red label the label of a phylotype is composed by its node identifier with its annotation Figure 8b Such phylotypes have a break in ancestral annotations meaning that there are ancestral annotations between the phylotype and its ancestor if one exists which are different from those of the ancestor and the phylotype This information corresponds to the AnB column of
16. e Naming the analysis at each run Figure 5 3 e Setting a number of iterations for the shuffling process strongly recommended Figure 5 4 e Selecting the method to compute ancestral annotations either ACCTRAN or DELTRAN Figure 5 5 Once PhyloType parameterization is complete click on the Go button PhyloType analysis is fast so don t hesitate to tune your parameterization over multiple analyses For instance start by using only the required criteria with their default thresholds With respect to the results overview table Figure 6 rerun the analysis with more or less stringent thresholds or add remove criteria Shuffling is highly recommended Hint Start your analysis with 100 iterations for example and use 1 000 iterations once your PhyloType parameterization seems appropriate Remember to rename the analysis at each new computation PhyloType User Manual v1 4 Page 10 Phylolype Interface PhyloType Home Interface User Guide Supplementary Material Tools input Annotation Analysis PhyloType settings and analysis PhyloType parametization selection of annotations and analyse PhyloType parameters ea Size S57 gt f Persistence Ps F 7 Size Different Sz Df i i O Different Df p O Local separation Sl Gar E O Global separation 5g bor i 7 Diversity Dv Do Local sep Diversity SUDv gt fp M Global sep Diversity Samh m Support Sp b7
17. e name VariableOl and then click on Go Select several values from the Country variable by clicking while holding the CTRL key Then click on add value s with an OR connector target the new variable to fill VariableO1 and then enter a name for a new annotation Africa Click on Go VariableO1 is now filled at 41 4 The corresponding sequences have the value Africa for VariableO1 in place of the selected values of the variable Country To fill VariableO1 at 100 click on add remaining values select the source and the target variables Country and Variable01 respectively and then click on Go For each sequence in the tree if there is no annotation value from VariableO1 it is then copied from the corresponding value of the Country variable VariableO1 is now ready to be used in a PhyloType analysis Page 9 5 The Analysis step The Analysis step corresponds to PhyloType parameterization computation and access to an overview of the results PhyloType parameterization is comprised of e Setting thresholds for the required criteria Sz Ps and Sz Df Figure 5 1 e Adding further criteria with more or less stringent thresholds e Selecting the variable to analyze Figure 5 2 e Selecting variable s annotations to analyze Ctrl A to select all annotations or use your mouse and the Shift Ctrl keys to add remove values
18. from at least two variables primary or new PhyloType checks for each combination between them If the combination exists that is for a given tip the values for the different variables are in the user s selection then a new annotation is inserted in the targeted variable Rename one or several annotation s from a new annotation The new name is chosen by the user This control enables the aggregation of annotations see also the control add value s with an OR connector Select one or several annotation s from a variable which is in the New annotations section primary annotations cannot be modified then enter a new name for the new annotation and click on the Go button This updates the New annotations section Select the control then select one or several annotations from a variable that is in the New annotations section primary annotations cannot be modified then click on the Go button This updates the New annotations section Page 8 Annotation example input Tree Defining new annotations to be explored optional Select and cormmiune annofatons fo define the annotations fo be used DY Primary annotations Continent Arica 106 41 4 Ase 11 Rai Europe 54 0 7 n ah MidE ast 1 SouthAmerica 87 33 3 UK 54 20 7 z ZA 37 142 z i G create a new variable with the name Varats0 p A C Spise vibe Coury z paaa t Primary annctatoos New annotabors Continent Co A Y
19. lumns are separated by a comma and values are in quotes PhyloType User Manual v1 4 Page 3 Integrating data sets The PhyloType interface Figure 2 includes examples of data sets To use one of these examples click the corresponding Load example button This fills the Tree and Annotations text areas with the corresponding data To use Copy Paste to integrate your data edit your tree and annotation files with any text editor and then copy paste the Newick string and annotations to the corresponding text area To use the Upload process click on the Upload link and then select the tree and annotation files you want to upload Use the Reset button at the bottom of the screen to clear all text area if necessary or use the scissors control a to clear a specific area You may not mix Copy Paste and Upload processes e g copy paste a tree and upload annotations Lastly to complete the Input step submit the data by clicking the arrow button and manually select the next tab in the PhyloType pipeline Tree PhyloType home ipssrtaca lisar Gwite teput i Annmotaltnn Anahy ns Owvtpyt ripest tate nput data Wee and annotations Sy CopePast ar Oy Usinogg Trees to Oe analysed must pem Howick format Trees must De rooted wih care o macpoinl rooted and contain Oranch lengths Trees can contain supper walues such as Soctsrap poslenor protabdties and lieplinood rate supports Amnotations to be analysed muat be formated as CSY Coma Sapagi
20. mary ci w Figure 4 Screenshot of the PhyloType Web interface the Annotation step PhyloType User Manual v1 4 Page 7 Table 1 Controls to build new annotations in the table below the character marks an input create a new variable with the name duplicate variable to EY delete variable add value s selection from one variable only to add remaining value s from to add value s with an OR connector selection from one variable only to name add value s with an AND connector multiple variables selection to rename value s primary annotations cannot be modified with name Remove one or several annotations selected by the user PhyloType User Manual v1 4 To build a new annotation variable select the control enter a name by default PhyloType generates new names starting with an A then click on the Go button The new variable is listed in the New annotations section Here the domain value of this new variable is still empty Creation of a new annotation variable by copying an existing one either a primary variable or a new variable after copying it is possible to modify its domain of values Select the control enter a name for the new variable then click on the Go button Select the control select a variable to delete only variables from the New annotations section can be deleted then click on the Go b
21. nce the phylotype map you have access to the phylotype map with the same Sz p value threshold You can also access a phylotype map with another p value threshold by using the Sz p value threshold menu again Each phylotype has a unique number in the first column named Pi Figure 7 3 This number is the node identifier from the tree linked to the root of phylotype The second column named Anc is a phylotype identifier ancestor to the phylotype In this example the phylotype Pi 1 Africa is the ancestor of two other phylotypes phylotype Pi 251 EastEurope and phylotype Pi 14 Greece The phylotype Pi 1 does not have phylotype ancestor then the Anc value is set to root The third column named A is the associated annotation The associated background color is specific to each phylotype and is the same as that used with the other outputs phylotype map and tree with color encoded phylotypes The Cov column displays the percentage of taxa annotated with the corresponding annotation that belongs to the phylotype In this example 88 of the Africa sequences in the tree belong to the phylotype Pi 1 The following columns are related to the values for all the PhyloType criteria If a shuffling process was used p values are shown in magenta only for the criteria used in the identification process except for Sp and Spg criteria Figure 7 4 The S column gives the list of strains inside a phylotype Figure 7 5 The
22. og Valta The fratrow contains Te names of the variatles to be analysed The frst variabie iret column must be he tana names case sensitne it for usnog the datacel tom Sy Pat _ Load example 1 d Saami et a 2008 Trees i Copy ante erm Annotations Conn Paste Mere 3 Baro gata Ooo oeal the maned as CSV The tral row cantaira two vanhatle s name Pw Gref vara Gri Column must be Me tp ladata Second COMM MUS De Pa Gite MurnDers w anampi Figure 2 Screenshot of PhyloType Web interface the Input step PhyloType User Manual v1 4 Page 4 3 The Tree step The second step of a PhyloType analysis is related to tree rooting Figure 3 This step is optional There are several methods for tree rooting with PhyloType see below If necessary select one of these methods by checking the corresponding option click on the Go button and then wait for the feedback message You may return to the submitted tree at any time by clicking on Root reset PhyloType flame itittartece User Gute Analysis Ouar Figure 3 Screenshot of the PhyloType Web interface the Tree step There are two parts to the tree display window the left part is a global view the right part is a local view a zoom in perspective Move the blue rectangle from the global view to navigate the local view Resize the blue rectangle by grabbing the bottom right corner to modify the zoom factor Methods available for rooting the tree e Va
23. oot this combination is always larger than the original local separation value and places more emphasis on the local separation of the phylotype than on those of its ascendants Dv S _ diversity average root to tip distance among phylotype strains SI Dv fe ratio of local separation S and diversity Dv ret ratio of global separation Sg and diversity Dv support e g bootstrap of the phylotype global support value of a weighted combination of local support starting from the phylotype root and considering all its ascendants all the way to the tree root this combination is always larger than the original local support value and places more emphasis on the local support of the phylotype than on those of its ascendants IV IA IV IV IV Ag 2 tQ PhyloType User Manual v1 4 Page 13 6 The Output step The Output step of the PhyloType pipeline covers the detailed results of a PhyloType analysis These details results are 1 a list of phylotypes 2 a phylotype map 3 trees with color encoded phylotypes and 4 trees with color encoded ancestral annotations 6 1 Phylotype table The table lists all phylotypes found by the analysis Figure 7 If a shuffling process was used the detailed list displays phylotypes for a given Sz p value threshold You can switch to another p value threshold by using the corresponding menu Figure 7 1 If you switch to another kind of output Figure 7 2 for insta
24. rersrrenrrensrersrtessrresreesrerese Tree with color coded ancestral ANNOtAtIONS cssssecccecsessececccaeesecccceeeeseeecsseaeeeeesauaesses Page 1 1 Overview PhyloType analysis is based on five steps Figure 1 Input Tree Annotation Analysis and Output e The nput step handles the input of a tree and annotations e The Tree step is optional enabling tree rooting if needed e The third step Annotation is also optional It enables combining the submitted annotation to define new annotations to be used by PhyloType e The Analysis step corresponds to the analysis itself including parameterization selection of annotations selection of criteria thresholds number of shuffling iterations and so on e Output isthe last step of the PhyloType pipeline giving access to the detailed output of an analysis table of phylotypes found tree graphics with color coded phylotypes table of annotation etc All output is downloadable Input Tree Annotation Analysis Output PhyloType Combine parametrization Copy paste or primary upload tree and Tree annotations to Annotation primary rooting and define selection annotations visualization annotations to be used by Analysis PhyloType Results Phylotype listing Tables Graphic views Results overview Aimo taton Analysis Output input data 7 i fee and Ivnnary FeQvuerc ammo x Click Load example 1 for using Me dataset trom Salem ef a 2008 A Click Load exemp L 20
25. riance minimization method This algorithm places the root on the point that minimizes the variance of each genetic distance between tips to this point PhyloType User Manual v1 4 Page 5 e Variance minimization with heterochronous tips method This algorithm is quite similar to the previous one except that it assumes that tips are not all contemporary To run it needs the sampling dates of each tip It places the root on the point that minimizes the variance of distances between each tip see like contemporary to this point To use this method submit dates by copy paste in the Dates text area where each tip from the tree is placed with respect to the date value separated by a colon without space Outgroup method The outgroup method lets you select one or more tips PhyloType roots the tree at 50 of the stemming branch of the ancestor of the selected tips To visualize the tree click on the Draw tree button Branch lengths and support values can be posted by checking on the corresponding box After rooting the new Newick string will be available for download in the Output section Proceed to the Annotation step by clicking the arrow button and selecting the next tab in the PhyloType pipeline Annotation PhyloType User Manual v1 4 Page 6 4 The Annotation step The Annotation step is optional It enables the selection and combination of submitted annotations to define new annotations to be used by PhyloType Figure 4 The
26. utton The New annotations section is updated On the control and target check the variable you want to fill with new annotations Before clicking on the Go button you must select one or several annotation s This selection operates from one variable only either from the Primary annotations or New annotations sections Complete the domain values of a new annotation variable Knowing an annotation variable to complete it fills its missing values from an annotation source selected by the user either a primary or a new annotation variable Select the control select the annotation variable you want to use as a source for annotation select the target variable you want to complete and then click on the Go button This updates the New annotation section A target annotation variable is filled with a new annotation for each selected annotation of one another variable either a primary or a new variable For instance knowing two annotation variables X a primary variable and Y a new variable to fill where X has the following annotations values x1 x2 x3 x4 x5 If x2 x3 and x4 are the selected annotations from X and the Y variable is selected as the targeted new variable to complete with the annotation x234 named by the user for each tip matching the value x2 OR x3 OR x4 from the variable X the Y variable is completed with the annotation x234 The OR connector enables the aggregation of annotations Knowing a selection of annotations
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