SylvX User's Manual 1.0
Contents
1. Acco o tothe output i C Lk es kel e trigonata_O Neotropics Ra Y J 4 b b el ed gi S PS or Scalable Vector Graphics SVG select the corresponding menu and target the map to be exported2. we we we We o o ooo ingens_31 T 4 32 religiosa_30 1 mollior 27 j uncinata_25 condensa 24 EN 1 x 7 wassa 21 3S 2 tinctoria 20 iv racemigera 18 fulva 16 deltoidea 14 odoardii 13 menabeensis 9 calophylla 7 annulata 6 obliqua 5 ovata 2 natalensis 1 trigonata 0 A new map is displayed with the same species tree mmm H H Display two reconciliations 2 2 first target the map 2 only and then target the new reconciliation to be displayed on Map 2 LL 1266782112 E OUTGROUP 39 glabrata 36 insipida 35 13 ingens 31 DE j 12 religiosa 30 api 23 mollior 27 h E K 21 condensa 24 35 wassa 21 34 tinctoria 20 H racemigera_18 2 fulva 16 deltoidea 14 odoardii 13 menabeensis 9 se aC DITALICOR mri SE calophylla_7 annulata 6 obliqua 5 Species tree ovata 2 21 s natalensis 1 C e Tools Annotation Si Annotate 8 SylvX v 18 SylvX Interface overview Map s toolbox tools working on species trees AND reconciliations O1 scenarios R GC c DITILICOR mr14266782 4 Rec D1T4L1COR mr14266782 Rec DOTILOCOR mr14266782 xec D1T1LOCOR mr14266782 d zl cc mm 2 q wo ec G er Reconcilation s toolbox Species Tree e toolbox MAP 1 Rec D1T4L1COR mr14266782112 DUP 2 LOS 6 TRA 8 rr m 1 EN BC Re
3. 05 x MAP 1 Rec_D1T4L1COR mr14267738622 MAP 2 Rec DOT1LOCOR mr14267738623 OUTGROUP 39 J UP 2 LOS 6 TRA 8 DUP 18 LOS 66 TRA 0 g abrata 36 curenou s na e Neotropics is 35 glabrata 36 p e EN 23 25 Neotropics pw agens 31 Afrotropics A insipida_35 13 15 D m f ingens 31 Afrotropics Aen 12 Ee Md 13 tk 3 as n D religiosa_30 Oriental 29 molior 27 Australasia r Compute 12 Mowgli 23 mollior 27 Australasia 153 go uncinata 25 Oriental Select Species tree 4 h ag uncinata 25 Oriental d z condensa 24 Oriental Australasia Select Gene tree file 34 Condensa 24 Oriental_Australasia y 35 wessa_21 Cost of duplication 1 35 wassa_21 S i he Onental Australasia Ss 34 tinctoria_20 Cost of transfer m Oriental Australasia M Cost of loss 2 1 34 tinctoria 20 Cost of cospeciation 0 racemigera 18 Ausiralasia Hill dimbing search x dimbing g lacemigera 18 Australasia F b z 2 fulva 16 Oriental 21 fulva 16 Oriental Cp S de k 49 Getoidea_14 Oriental 19 deltoidea 14 Oriental LU Hi aW 27 a E gum odoardi 13 Oriental Australasia odoardii 13 Oniental Australasia n menabeensis 9 Afrotropics e menabeensis 9 Afrotropics x calophylla 7 calaphyils 7 1 Oriental Oriental annulata 6 annulata 6 2 2 k obliqua_5 Australasia Q omes Australasia E Et 4 E e n e S ovata 2 1 S th E l tab Bs 1 x es Afrotropics 6 x67 E natalensis 1 2 e e m
4. 42 religiosa 30 23 mollior 27 ap uncinata 25 21 condensa 24 35 wassa 21 34 tinctoria 20 H racemigera_18 21 fulva 16 Rec DiTIL1COR mr E TE Rec D1T4L1C0950r14266782 28 ie cS 19 X deltoidea 14 Rec DOT1LOCORAEBBSSZ C os Rec D1T1LOCOR 27 odoardii 13 Ce menabeensis_9 cc mm 2 d es 2 annulata 6 q obliqua 5 4 ovata 2 ec DTTILTCOR mr14266782 S raens 1 e fale ef af d m Zen 7 l SITE AOL RY trigonata 0 A i u ee s 9 ka HB Display another reconciliation target another reconciliation LB SylvX v 18 File Edit MAP 1 Rec_DOT1LOCOR mr14266762113 GA DUP 18 LOS 66 Rec DITILICOR oh p Rec LE o ga gi s de c WRec DITILOCOR R li e T ae y E v LIES 0 M t etc RK Annotate 128 Rec DOT1LOCOR mr1 ja 162 Gei E s BTEC mr14266782 zi IDX B OUTGROUP 39 glabrata 36 insipida 35 ingens 31 religiosa 30 mollior 27 uncinata 25 condensa 24 wassa 21 tinctoria 20 racemigera 18 fulva 16 deltoidea 14 odoardii 13 menabeensis 9 calophylla 7 annulata 6 obliqua 5 ovata 2 natalensis 1 trigonata 0 H Display two reconciliations 1 2 add a map S SylivX v 18 all xi Fie Edit MAP 1 Rec DOT1LOCOR mr14266782113 MAP 2 DUP 18 LOS 66 TRA 0 E Lo nd OUTGROUP_39 gu d P glabrata_36 M EOELLAOAULGI amp uuu uL I insipida 35 rr 0 we we
5. 6 TRA 8 OUTGROUP 39 23 glabrata 36 i 24 insipida 35 ingens 31 am religiosa 30 29 mollior 27 ap uncinata 25 31 condensa_24 35 wassa 21 34 tinctoria 20 H racemigera_18 21 fulva 16 34 19 deltoidea 14 Open Annotation Regarder dans DataTols 77 odoardii 13 8 ex EZ Modifi le sl Tyr T 31 05 2013 13 14 Fichier TXT Emplacements 16 05 2013 20 23 Fichier MR recents 16 05 2013 20 22 Fichier MPR annulata 6 o obliqua 5 5 menabeensis 9 calophylla 7 ovata 2 Biblioth ques e natalensis_1 lt trigonata 0 A m Ordinateur Load an annotation file Species tree and annotations combination m Sylvx v 18 ll xl File Edit MAP 1 Rec D1TA4L1COR mr14267738622 DUP 2 LOS 6 TRA 8 OUTGROUP 39 B ais 1 Select an pose annotation e g pul Geography a zez 2 Select a command poe e g Subtree P oam Text color 25 35 wassa 21 34 tinctoria 20 0 racemigera 18 21 fulva 16 vg deltoidea 14 Rec DOT1LOCOR mr14267738 Rec D1T1LOCOR mr14267738 odoardii 13 zc mm 2 g en EA ec SSC alm Species tree o f Taxo sp S e el MEISTE n r Annotation axo genus 19 deltoidea_14 Onental d Onental Australasia 34 tinctoria 20 racemigera 18 Australasia Onental 21 fulva 16 Taxo spill z G
6. SylvX User s Manual 1 0 E Jousselin amp F Chevenet Launch SylvX Data to Load 1 2 load the species tree Data to Load 2 2 load a reconciliation file Display a reconciliation 1 2 target a map Display a reconciliation 2 2 select a reconciliation Display another reconciliation target another reconciliation Display two reconciliations 1 2 add a map Display two reconciliations 2 2 display the reconciliation SylvX Interface overview Map toolbox overview Reconciliation s toolbox overview Species tree toolbox overview Species tree and annotations combination Data to Compute with Mowsli 1 3 select the species tree Data to Compute with Mowgli 2 3 select the gene tree Data to Compute with Mowsli 3 3 Mowgli settings and run Output graphics Launch SylvX EE syivx v 18 Bl x Nom P Ji data Ji Mowgli ka sylvx exe All the SylvX s controls are on the left side of the interface Data to Load 1 2 load the species tree ES DataToLoad 8 sylvx v 18 A Ordinateur T Modifi le E 16 05 2013 20 38 Fichier TXT EE Fichier MR 5 05 2013 20 22 Fichie Tw qe Ef mad S CC Types de fichiers AI Files 7 DI 7 Data to Load 2 2 load a reconciliation file EE SylvX v 18 EN iBl xl cdi MAP 1 P OUTGROUP 39 L3 Open glabrata 36 insipida 35 ingens 31 Nom religiosa 30 i data mollior 27 A Mowgli uncinata_25 H con
7. conciliation olor coded 7 Arrow tranf inl x E OUTGROUP_39 glabrata_36 insipida_35 ingens 31 religiosa 30 mollior 27 uncinata 25 condensa 24 wassa 21 tinctoria 20 racemigera 18 fulva 16 deltoidea 14 odoardii 13 menabeensis 9 calophylla 7 annulata 6 obliqua 5 ovata 2 natalensis 1 trigonata 0 Map toolbox overview NS e ey C A o SS w Tools v Add a new map the species tree is automatically displayed The menu displays all the available maps Select a map to delete it Each map has a color ID up right corner of each map Each map has also a zooming brush using the corresponding color Left click the circle down right corner and drag it to resize the brush and set a zooming factor Select the brush border to move it left click and drag The corresponding map is updated following the position and size of its brush Tools to be activated left clic then apply manually on map s From left to right up to down fit to window left clic on the map Magnify left clic and drag to display a frame which will be used to zoom in the map Zoom Out Zoom In Zoom Out only x Zoom In only x Zoom Out only y Zoom In only y Command tools working on the current map selection Map targetting menu This menu lists all the available maps A map can be selected or unselected The selection is inclusive Target a map before selecting a reconciliation Reconci
8. de 24 FB sylvx exe m wassa 21 tinctoria 20 racemigera 18 go a BS n data B fulva 16 Ei Q deltoidea_14 odoardii 13 menabeensis 9 Nom E ne l 16 05 2013 20 38 Fichier TXT calophylla 7 i DataToCompute Run Emplacements 16 0 5 20 1 3 20 23 Fichier MR r cents 16 05 2013 20 22 Fichier MPR annulata 6 DataToLoad obliqua 5 ovata 2 natalensis 1 Biblioth ques trigonata 0 A Select and open the R mpr file The R mpr contains 4 reconcilia R seau 4 Ill gt Display a reconciliation 1 2 target a map sylvx v 18 iani x RE ca MAP 1 E OUTGROUP 39 mm Remove y Ej P glabrata_36 insipida 35 ingens 31 religiosa_30 mollior_27 e 5 28 uncinata 25 ca Q Q l l condensa_24 RAQA wassa 21 Tools 4 E a tinctoria_20 Map 1 l Select all A p racemigera_18 C UnSelect all E H Ceriarios i fulva_16 Rec D1T1L1COR mr142667827 e deltoidea 14 Rec D1T4L1COR mr14266782 15 Rec DOT1LOCOR mr14266782 odoardii 13 iv Fa Rec D1T1LOCOR mr14266782 menabeensis 9 iv DH cc mm 2 d calophylla 7 annulata 6 obliqua 5 ovata 2 natalensis 1 trigonata 0 Display a reconciliation 2 2 select a reconciliation s Sylvx v 18 Eije 3 File Edit MAP 1 Rec_D1T4L1COR mr14266782112 DUP 2 LOS 6 TRA 8 OUTGROUP 39 23 glabrata 36 g insipida 35 13 ingens 31
9. eogr phy axo genus odoardii_13 Onental_Australasia 5 5 menabeensis 91 Afrotropics calophylla 7 d l i 3 Oriental D a_i annulata_6 2 2 obliqua_5 Australasia Subtree Text color mmm el colc AS i Subtree Foreground Reset annotation Data to Compute with Mowsli 1 3 select the species tree ll x a Modifi le dn zl E wn 70 0 0 0 0 wes e delye t Eg G txt 06 04 2012 15 05 Fichier TXT Emplacements che r 06 04 2012 15 04 Fichier TXT Data to Compute with Mowgli 2 3 select the gene tree SylvX v 18 inl xl me Bo Open a gene tree x d d Emplacements r cents Z Bureau e E wa in a yal Biblioth ques e Data to Compute with Mowgli 3 3 Mowgli settings and run As soon as Mowgli Seo BER returns its output ge SylvX switches to Edit Mode and the new reconciliation is available in the reconciliation listbox select it to dispay it in the current targeted map s OUTGROUP_39 glabrata_36 insipida_35 ingens_31 religiosa_30 mollior_27 ot Ii Rec_ 1F ufeconciliation mpr14266875121 m 12 i RUP 0 LOS 1 TRE 10 Output graphics In sylvx v 18 E E g 1
10. liation s toolbox overview Dash line Left clic the tool to activate it then apply it on the fly to internal nodes of a reconcialiation to set on off dash line of the corresponding subtree Line width Left clic the tool to activate it then apply it on the fly to internal nodes of a reconcialiation to set increase decrease Shift left clic the line width of the corresponding subtree Reconciliation s UC scenarios EE 82 Rec D1T4L1COR mr142667 Rec DOT1LOCOR mr1426678 Rec D1T1LOCOR mr14266 Foreground color Left clic the tool to activate it then apply it on the fly to internal nodes of a reconcialiation to set increase decrease Shift left clic the line width of the corresponding subtree E Ar I Shrink Left clic the tool to activate it then apply it A a on the fly to internal nodes of a reconcialiation to s LQ hide the corresponding subtree including transfert events Sie Jools Information Left clic the tool to activate it then apply it to an internal node of a reconciliation to insert an annotation Information Left clic the tool to activate it Display Hide then apply it to internal node of the species Expand v1 tree to expand underlying duplications Expand by duplication Expand by transfert Move subtree Left clic the tool to Commands working on the activate it then apply it on the fly to a Color whole sprecies trees segment of a
11. reconciliation to move the f targeted ones underlying subtree esie eem Move segment Left clic the tool to activate it then Dozens apply it to the segments of a reconciaiation to move it Line size 1 including transfer events The translation is local Line size 2 Line size 3 Gene node b Species tree toolbox overview Swap left clic the tool to activate it then apply it left clic to internal nodes of the species trees note that this operation resets the tree with its reconciliation Line width left clic the tool to activate it then left clic species tree segments to increase their sizes or Shift left clic to decrease their sizes Foreground color Left clic the tool to activate it then select a color and apply it To the species tree segments Fit to contents Information Left clic the tool to activate it then apply it to internal node of the species tree to insert an annotation Tha odoardii 13 gt gt gt gt gt reached menabeensis 9 1 calophylla 7 1 5 e menabeensis annulata 6 1 obliqua 5 1 FECI ovata 2 1 1 nn natalensis 1 1 3 trigonata 0 1 annulata 6 2 gt gt gt gt gt not reached empty E obliqua 5 4 ovata 2 m 6 natalensis 1 LR 1 41 trigonata 0 0 Commands working on the whole species trees targeted ones Species tree and annotation combination CE Syivx v 18 Fie Edit MAP 1 Rec D1T4L1COR mr14267738622 DUP 2 LOS
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