search

talgalili / dendextend

Extending R's Dendrogram Functionality
152 stars 28 forks source link

Error: argument is of length zero #92

Open dezordi opened 5 years ago

dezordi commented 5 years ago

library(ape) library(dendextend) tree1 <- read.tree(file='/home/bioinfo/Desktop/tree_element.txt') is.rooted(tree1) tree2 <- read.tree(file='/home/bioinfo/Desktop/tree_glyco.txt') is.rooted(tree2) den1 <-chronos(tree1) den2 <-chronos(tree2) tanglegram(den1,den2)

output: Error in if (new_labels_length < leaves_length) { : argument is of length zero

if I:

>den1 output: Chronogram Call: chronos(phy = tree1) Phylogenetic tree with 86 tips and 85 internal nodes. Tip labels: AAeliv_16, AegAag2_31, AegAag2_33, AAlC636_02, AAlC636_03, AAlC636_36, ... Rooted; includes branch lengths.

or

>den2 output: Chronogram Call: chronos(phy = tree2) Phylogenetic tree with 86 tips and 85 internal nodes. Tip labels: AAlC636_19, AAlC636_38, AAlFosh_06, AegAag2_39, AegAag2_03, CQuJoh_04, ... Rooted; includes branch lengths.

Is it a common error? I already make other tanglegrams with the same arguments, in this same computer with the same R version (version.string R version 3.4.4 (2018-03-15)).

Thanks for your attention.

talgalili commented 5 years ago

I'd suggest to use as.dendrogram on each object first and see if there is a problem there. If there isn't I'd look at the plot of each of the as.dendrogram objects to see if the trees have any issues. Also, look at setdiff of the labels of each tree (they both must have the exact same set of labels).

Hope this helps.

On Thu, Apr 25, 2019 at 3:54 AM dezordi notifications@github.com wrote:

library(ape) library(dendextend) tree1 <- read.tree(file='/home/bioinfo/Desktop/tree_element.txt') is.rooted(tree1) tree2 <- read.tree(file='/home/bioinfo/Desktop/tree_glyco.txt') is.rooted(tree2) den1 <-chronos(tree1) den2 <-chronos(tree2) tanglegram(den1,den2)

output: Error in if (new_labels_length < leaves_length) { : argument is of length zero

if I:

den1 output: Chronogram Call: chronos(phy = tree1) Phylogenetic tree with 86 tips and 85 internal nodes. Tip labels: AAeliv_16, AegAag2_31, AegAag2_33, AAlC636_02, AAlC636_03, AAlC636_36, ... Rooted; includes branch lengths.

or

den2 output: Chronogram Call: chronos(phy = tree2) Phylogenetic tree with 86 tips and 85 internal nodes. Tip labels: AAlC636_19, AAlC636_38, AAlFosh_06, AegAag2_39, AegAag2_03, CQuJoh_04, ... Rooted; includes branch lengths.

Is it a common error? I already make other tanglegrams with the same arguments, in this same computer with the same R version (version.string R version 3.4.4 (2018-03-15)).

Thanks for your attention.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/talgalili/dendextend/issues/92, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHOJBRABKR7DO2VGD2OHJLPSGEW7ANCNFSM4HIL7LIA .

dezordi commented 5 years ago

I found the error, several branches have the branch length equal to 0, it explains the 'argument is of length zero'.

Moreover, I didn't find a parameter to plot branch support values in a tanglegram, there is any parameter to do this?

Thanks.

theo-llewellyn commented 5 years ago

I have the same problem using trees that have some branch lengths = 0. Is there a way around this?

talgalili commented 5 years ago

Hey, What happens if you use: raise.dendrogram(dend, 0.01) in the input of the dendrogram with a branch of height 0?

On Mon, Jul 8, 2019 at 6:12 PM theo-llewellyn notifications@github.com wrote:

I have the same problem using trees that have some branch lengths = 0. Is there a way around this?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/talgalili/dendextend/issues/92?email_source=notifications&email_token=AAHOJBTQNWMVJV25YKMGTMLP6NRONA5CNFSM4HIL7LIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZNSVZQ#issuecomment-509291238, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHOJBTR24FH7VQB42OVE2LP6NRONANCNFSM4HIL7LIA .

theo-llewellyn commented 5 years ago

Hey, thanks for the reply. When I call raise.dendrogram(dend, 0.01) on the dendrogram I get the following error:

Error in attr(dend, "height") <- attr(dend, "height") + heiget_to_add : attempt to set an attribute on NULL

talgalili commented 5 years ago

Any chance for a self contained code I can run to reproduce this error? Maybe use dput to export the object?

On Tue, Jul 9, 2019, 16:48 theo-llewellyn notifications@github.com wrote:

Hey, thanks for the reply. When I call raise.dendrogram(dend, 0.01) on the dendrogram I get the following error:

Error in attr(dend, "height") <- attr(dend, "height") + heiget_to_add : attempt to set an attribute on NULL

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/talgalili/dendextend/issues/92?email_source=notifications&email_token=AAHOJBSZL6LWDXC5OPNEHG3P6SQKTA5CNFSM4HIL7LIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZQQB5A#issuecomment-509673716, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHOJBXSFBJNRMBFFIJZYXTP6SQKTANCNFSM4HIL7LIA .

theo-llewellyn commented 5 years ago

library(ape) library(dendextend)

ASTRAL_tree <- read.tree(file.choose()) chronos_ASTRAL <- chronos(ASTRAL_tree) dendr <- as.dendrogram(chronos_ASTRAL) raise.dendrogram(dendr, 0.01)

This is the code I ran. Is this sufficient or would you also need the tree file I use?

talgalili commented 5 years ago

I'll need the tree file. Or paste the output of dput(chronos_ASTRAL)

On Tue, Jul 9, 2019, 17:23 theo-llewellyn notifications@github.com wrote:

library(ape) library(dendextend)

ASTRAL_tree <- read.tree(file.choose()) chronos_ASTRAL <- chronos(ASTRAL_tree) dendr <- as.dendrogram(chronos_ASTRAL) raise.dendrogram(dendr, 0.01) This is the code I ran. Is this sufficient or would you also need the tree file I use?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/talgalili/dendextend/issues/92?email_source=notifications&email_token=AAHOJBSQ5TJF6CEH7UGH7SLP6SUONA5CNFSM4HIL7LIKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZQTUHQ#issuecomment-509688350, or mute the thread https://github.com/notifications/unsubscribe-auth/AAHOJBT3245MZR75UM3TEWLP6SUONANCNFSM4HIL7LIA .

theo-llewellyn commented 5 years ago

structure(list(edge = structure(c(380L, 381L, 382L, 383L, 383L, 382L, 384L, 385L, 385L, 384L, 386L, 386L, 381L, 387L, 388L, 388L, 387L, 389L, 390L, 390L, 389L, 391L, 391L, 392L, 392L, 380L, 393L, 394L, 394L, 395L, 395L, 396L, 397L, 397L, 396L, 398L, 399L, 399L, 398L, 400L, 400L, 401L, 401L, 402L, 402L, 393L, 403L, 404L, 405L, 406L, 406L, 405L, 407L, 407L, 408L, 408L, 409L, 409L, 404L, 410L, 411L, 411L, 412L, 413L, 413L, 414L, 415L, 415L, 414L, 416L, 417L, 417L, 418L, 418L, 419L, 419L, 416L, 420L, 420L, 421L, 421L, 422L, 422L, 412L, 423L, 424L, 424L, 425L, 425L, 426L, 426L, 423L, 427L, 428L, 428L, 429L, 429L, 430L, 430L, 431L, 431L, 427L, 432L, 433L, 433L, 434L, 434L, 432L, 435L, 435L, 436L, 437L, 437L, 436L, 438L, 438L, 439L, 439L, 410L, 440L, 441L, 442L, 442L, 443L, 443L, 444L, 444L, 441L, 445L, 446L, 446L, 445L, 447L, 447L, 448L, 448L, 440L, 449L, 450L, 451L, 451L, 450L, 452L, 452L, 453L, 453L, 454L, 454L, 449L, 455L, 456L, 456L, 455L, 457L, 458L, 459L, 459L, 460L, 460L, 461L, 461L, 458L, 462L, 463L, 464L, 464L, 463L, 465L, 466L, 466L, 465L, 467L, 467L, 468L, 468L, 462L, 469L, 470L, 470L, 469L, 471L, 472L, 472L, 473L, 473L, 474L, 474L, 471L, 475L, 476L, 476L, 475L, 477L, 477L, 478L, 478L, 457L, 479L, 480L, 480L, 481L, 481L, 482L, 482L, 479L, 483L, 484L, 484L, 485L, 485L, 483L, 486L, 487L, 487L, 488L, 488L, 486L, 489L, 490L, 491L, 491L, 492L, 492L, 493L, 493L, 490L, 494L, 494L, 495L, 495L, 496L, 496L, 489L, 497L, 498L, 498L, 499L, 499L, 500L, 500L, 497L, 501L, 502L, 502L, 503L, 504L, 504L, 503L, 505L, 505L, 506L, 506L, 501L, 507L, 507L, 508L, 508L, 509L, 509L, 510L, 510L, 511L, 511L, 512L, 512L, 513L, 513L, 403L, 514L, 515L, 516L, 516L, 517L, 518L, 518L, 519L, 519L, 517L, 520L, 521L, 521L, 520L, 522L, 522L, 515L, 523L, 524L, 524L, 523L, 525L, 526L, 527L, 527L, 526L, 528L, 529L, 529L, 528L, 530L, 530L, 525L, 531L, 532L, 533L, 534L, 535L, 535L, 534L, 536L, 536L, 533L, 537L, 538L, 538L, 537L, 539L, 539L, 540L, 540L, 541L, 541L, 532L, 542L, 543L, 544L, 544L, 545L, 545L, 543L, 546L, 547L, 547L, 546L, 548L, 548L, 549L, 549L, 542L, 550L, 550L, 551L, 552L, 552L, 553L, 553L, 554L, 554L, 551L, 555L, 556L, 556L, 557L, 557L, 555L, 558L, 558L, 559L, 559L, 531L, 560L, 560L, 561L, 562L, 563L, 563L, 562L, 564L, 564L, 561L, 565L, 566L, 567L, 567L, 568L, 569L, 569L, 568L, 570L, 570L, 566L, 571L, 572L, 572L, 573L, 573L, 574L, 574L, 571L, 575L, 576L, 576L, 575L, 577L, 578L, 578L, 577L, 579L, 579L, 580L, 580L, 581L, 582L, 582L, 581L, 583L, 583L, 584L, 584L, 565L, 585L, 586L, 586L, 587L, 587L, 588L, 588L, 585L, 589L, 590L, 591L, 591L, 590L, 592L, 592L, 589L, 593L, 594L, 595L, 596L, 596L, 595L, 597L, 598L, 598L, 599L, 600L, 600L, 599L, 601L, 601L, 597L, 602L, 602L, 603L, 603L, 604L, 604L, 605L, 605L, 594L, 606L, 607L, 608L, 608L, 609L, 609L, 607L, 610L, 610L, 611L, 611L, 612L, 612L, 606L, 613L, 614L, 615L, 615L, 614L, 616L, 616L, 617L, 617L, 613L, 618L, 619L, 619L, 620L, 621L, 621L, 620L, 622L, 622L, 618L, 623L, 623L, 624L, 625L, 625L, 624L, 626L, 626L, 627L, 627L, 628L, 629L, 629L, 630L, 630L, 628L, 631L, 632L, 632L, 631L, 633L, 633L, 634L, 634L, 593L, 635L, 636L, 637L, 637L, 638L, 639L, 639L, 638L, 640L, 640L, 641L, 641L, 636L, 642L, 643L, 643L, 642L, 644L, 644L, 645L, 646L, 646L, 647L, 647L, 648L, 648L, 649L, 649L, 645L, 650L, 650L, 651L, 652L, 652L, 653L, 653L, 654L, 654L, 651L, 655L, 655L, 656L, 656L, 657L, 658L, 658L, 657L, 659L, 659L, 635L, 660L, 661L, 662L, 662L, 663L, 664L, 664L, 663L, 665L, 665L, 661L, 666L, 666L, 667L, 668L, 668L, 667L, 669L, 669L, 670L, 670L, 671L, 671L, 672L, 672L, 660L, 673L, 674L, 674L, 673L, 675L, 676L, 676L, 675L, 677L, 678L, 679L, 679L, 678L, 680L, 680L, 681L, 681L, 677L, 682L, 683L, 683L, 682L, 684L, 685L, 685L, 684L, 686L, 686L, 514L, 687L, 688L, 688L, 687L, 689L, 690L, 691L, 692L, 693L, 693L, 694L, 694L, 692L, 695L, 696L, 696L, 695L, 697L, 697L, 691L, 698L, 699L, 699L, 700L, 700L, 698L, 701L, 701L, 702L, 702L, 703L, 703L, 690L, 704L, 705L, 705L, 704L, 706L, 706L, 707L, 708L, 709L, 709L, 708L, 710L, 710L, 711L, 711L, 707L, 712L, 712L, 713L, 713L, 689L, 714L, 715L, 716L, 716L, 717L, 718L, 718L, 717L, 719L, 720L, 720L, 719L, 721L, 722L, 722L, 721L, 723L, 723L, 724L, 724L, 725L, 725L, 715L, 726L, 727L, 728L, 728L, 727L, 729L, 729L, 726L, 730L, 730L, 731L, 732L, 733L, 733L, 732L, 734L, 734L, 731L, 735L, 736L, 737L, 737L, 736L, 738L, 738L, 735L, 739L, 740L, 740L, 739L, 741L, 741L, 714L, 742L, 742L, 743L, 744L, 745L, 745L, 744L, 746L, 746L, 747L, 747L, 748L, 748L, 749L, 749L, 743L, 750L, 751L, 751L, 752L, 752L, 753L, 753L, 754L, 754L, 750L, 755L, 756L, 756L, 755L, 757L, 757L, 381L, 382L, 383L, 1L, 2L, 384L, 385L, 3L, 4L, 386L, 5L, 6L, 387L, 388L, 7L, 8L, 389L, 390L, 9L, 10L, 391L, 11L, 392L, 12L, 13L, 393L, 394L, 14L, 395L, 15L, 396L, 397L, 16L, 17L, 398L, 399L, 18L, 19L, 400L, 20L, 401L, 21L, 402L, 22L, 23L, 403L, 404L, 405L, 406L, 24L, 25L, 407L, 26L, 408L, 27L, 409L, 28L, 29L, 410L, 411L, 30L, 412L, 413L, 31L, 414L, 415L, 32L, 33L, 416L, 417L, 34L, 418L, 35L, 419L, 36L, 37L, 420L, 38L, 421L, 39L, 422L, 40L, 41L, 423L, 424L, 42L, 425L, 43L, 426L, 44L, 45L, 427L, 428L, 46L, 429L, 47L, 430L, 48L, 431L, 49L, 50L, 432L, 433L, 51L, 434L, 52L, 53L, 435L, 54L, 436L, 437L, 55L, 56L, 438L, 57L, 439L, 58L, 59L, 440L, 441L, 442L, 60L, 443L, 61L, 444L, 62L, 63L, 445L, 446L, 64L, 65L, 447L, 66L, 448L, 67L, 68L, 449L, 450L, 451L, 69L, 70L, 452L, 71L, 453L, 72L, 454L, 73L, 74L, 455L, 456L, 75L, 76L, 457L, 458L, 459L, 77L, 460L, 78L, 461L, 79L, 80L, 462L, 463L, 464L, 81L, 82L, 465L, 466L, 83L, 84L, 467L, 85L, 468L, 86L, 87L, 469L, 470L, 88L, 89L, 471L, 472L, 90L, 473L, 91L, 474L, 92L, 93L, 475L, 476L, 94L, 95L, 477L, 96L, 478L, 97L, 98L, 479L, 480L, 99L, 481L, 100L, 482L, 101L, 102L, 483L, 484L, 103L, 485L, 104L, 105L, 486L, 487L, 106L, 488L, 107L, 108L, 489L, 490L, 491L, 109L, 492L, 110L, 493L, 111L, 112L, 494L, 113L, 495L, 114L, 496L, 115L, 116L, 497L, 498L, 117L, 499L, 118L, 500L, 119L, 120L, 501L, 502L, 121L, 503L, 504L, 122L, 123L, 505L, 124L, 506L, 125L, 126L, 507L, 127L, 508L, 128L, 509L, 129L, 510L, 130L, 511L, 131L, 512L, 132L, 513L, 133L, 134L, 514L, 515L, 516L, 135L, 517L, 518L, 136L, 519L, 137L, 138L, 520L, 521L, 139L, 140L, 522L, 141L, 142L, 523L, 524L, 143L, 144L, 525L, 526L, 527L, 145L, 146L, 528L, 529L, 147L, 148L, 530L, 149L, 150L, 531L, 532L, 533L, 534L, 535L, 151L, 152L, 536L, 153L, 154L, 537L, 538L, 155L, 156L, 539L, 157L, 540L, 158L, 541L, 159L, 160L, 542L, 543L, 544L, 161L, 545L, 162L, 163L, 546L, 547L, 164L, 165L, 548L, 166L, 549L, 167L, 168L, 550L, 169L, 551L, 552L, 170L, 553L, 171L, 554L, 172L, 173L, 555L, 556L, 174L, 557L, 175L, 176L, 558L, 177L, 559L, 178L, 179L, 560L, 180L, 561L, 562L, 563L, 181L, 182L, 564L, 183L, 184L, 565L, 566L, 567L, 185L, 568L, 569L, 186L, 187L, 570L, 188L, 189L, 571L, 572L, 190L, 573L, 191L, 574L, 192L, 193L, 575L, 576L, 194L, 195L, 577L, 578L, 196L, 197L, 579L, 198L, 580L, 199L, 581L, 582L, 200L, 201L, 583L, 202L, 584L, 203L, 204L, 585L, 586L, 205L, 587L, 206L, 588L, 207L, 208L, 589L, 590L, 591L, 209L, 210L, 592L, 211L, 212L, 593L, 594L, 595L, 596L, 213L, 214L, 597L, 598L, 215L, 599L, 600L, 216L, 217L, 601L, 218L, 219L, 602L, 220L, 603L, 221L, 604L, 222L, 605L, 223L, 224L, 606L, 607L, 608L, 225L, 609L, 226L, 227L, 610L, 228L, 611L, 229L, 612L, 230L, 231L, 613L, 614L, 615L, 232L, 233L, 616L, 234L, 617L, 235L, 236L, 618L, 619L, 237L, 620L, 621L, 238L, 239L, 622L, 240L, 241L, 623L, 242L, 624L, 625L, 243L, 244L, 626L, 245L, 627L, 246L, 628L, 629L, 247L, 630L, 248L, 249L, 631L, 632L, 250L, 251L, 633L, 252L, 634L, 253L, 254L, 635L, 636L, 637L, 255L, 638L, 639L, 256L, 257L, 640L, 258L, 641L, 259L, 260L, 642L, 643L, 261L, 262L, 644L, 263L, 645L, 646L, 264L, 647L, 265L, 648L, 266L, 649L, 267L, 268L, 650L, 269L, 651L, 652L, 270L, 653L, 271L, 654L, 272L, 273L, 655L, 274L, 656L, 275L, 657L, 658L, 276L, 277L, 659L, 278L, 279L, 660L, 661L, 662L, 280L, 663L, 664L, 281L, 282L, 665L, 283L, 284L, 666L, 285L, 667L, 668L, 286L, 287L, 669L, 288L, 670L, 289L, 671L, 290L, 672L, 291L, 292L, 673L, 674L, 293L, 294L, 675L, 676L, 295L, 296L, 677L, 678L, 679L, 297L, 298L, 680L, 299L, 681L, 300L, 301L, 682L, 683L, 302L, 303L, 684L, 685L, 304L, 305L, 686L, 306L, 307L, 687L, 688L, 308L, 309L, 689L, 690L, 691L, 692L, 693L, 310L, 694L, 311L, 312L, 695L, 696L, 313L, 314L, 697L, 315L, 316L, 698L, 699L, 317L, 700L, 318L, 319L, 701L, 320L, 702L, 321L, 703L, 322L, 323L, 704L, 705L, 324L, 325L, 706L, 326L, 707L, 708L, 709L, 327L, 328L, 710L, 329L, 711L, 330L, 331L, 712L, 332L, 713L, 333L, 334L, 714L, 715L, 716L, 335L, 717L, 718L, 336L, 337L, 719L, 720L, 338L, 339L, 721L, 722L, 340L, 341L, 723L, 342L, 724L, 343L, 725L, 344L, 345L, 726L, 727L, 728L, 346L, 347L, 729L, 348L, 349L, 730L, 350L, 731L, 732L, 733L, 351L, 352L, 734L, 353L, 354L, 735L, 736L, 737L, 355L, 356L, 738L, 357L, 358L, 739L, 740L, 359L, 360L, 741L, 361L, 362L, 742L, 363L, 743L, 744L, 745L, 364L, 365L, 746L, 366L, 747L, 367L, 748L, 368L, 749L, 369L, 370L, 750L, 751L, 371L, 752L, 372L, 753L, 373L, 754L, 374L, 375L, 755L, 756L, 376L, 377L, 757L, 378L, 379L), .Dim = c(756L, 2L)), edge.length = c(0.82476824381564, 0.071857162402325, 0.0692112617218586, 0.0341633320601769, 0.0341633320601769, 0.0349884321108693, 0.0343487061787082, 0.034037455492458, 0.034037455492458, 0.0343487061787082, 0.034037455492458, 0.034037455492458, 0.0366691085759728, 0.104317349606824, 0.0342452980015636, 0.0342452980015636, 0.0355173878642192, 0.0689457810828463, 0.0340994786613222, 0.0340994786613222, 0.0347339153996328, 0.0683113443445357, 0.0342978652301531, 0.0340134791143826, 0.0340134791143826, 0.083167590031052, 0.674308723159371, 0.242523686809577, 0.036272487412608, 0.206251199396969, 0.0354385253049151, 0.136891745598347, 0.0339209284937075, 0.0339209284937075, 0.034796018010481, 0.102177225070822, 0.0338394310107518, 0.0338394310107518, 0.0343397146943085, 0.101676941387265, 0.0340611334878199, 0.0676158078994449, 0.0338707484834537, 0.0337450594159912, 0.0337450594159912, 0.0657786945800828, 0.200460861228172, 0.51574282450146, 0.101277246082854, 0.0335727835763793, 0.0335727835763793, 0.0339974216074871, 0.100852608051746, 0.0337611374293258, 0.06709147062242, 0.0335992353919142, 0.0334922352305058, 0.0334922352305058, 0.0386563272138364, 0.310253054109353, 0.301683472837504, 0.0342138724939087, 0.0672785526642253, 0.20019104767937, 0.0335324842658098, 0.133358951364515, 0.0332996120490445, 0.0332996120490445, 0.0334463741242415, 0.0333482636634495, 0.0998639256258689, 0.0333111316955705, 0.0665527939302984, 0.0332850680532809, 0.0332677258770175, 0.0332677258770175, 0.0333482636634496, 0.0998639256258688, 0.0333111316955704, 0.0665527939302985, 0.033285068053281, 0.0332677258770174, 0.0332677258770174, 0.0338164061544766, 0.133690923275263, 0.0999622709138559, 0.0333597149564607, 0.0666025559573952, 0.0333158724278236, 0.0332866835295715, 0.0332866835295715, 0.0336394861807518, 0.0668111446714353, 0.133202563336931, 0.0333498699123951, 0.0998526934245363, 0.0333094028156006, 0.0665432906089356, 0.0332810657777805, 0.0332622248311551, 0.0332622248311551, 0.0334741627800982, 0.0999813251536656, 0.0665582200746028, 0.0332910966087586, 0.0332671234658441, 0.0332671234658441, 0.0333866169239626, 0.133152928304306, 0.0333365199770871, 0.0665580064175568, 0.0332584019096619, 0.0332584019096619, 0.0332941074451328, 0.0665223008820858, 0.0332693786377292, 0.0332529222443566, 0.0332529222443566, 0.037123726423991, 0.441075657152493, 0.0335849357721146, 0.100152207598257, 0.0334604138525807, 0.0666917937456768, 0.0333744345113351, 0.0333173592343417, 0.0333173592343417, 0.0335980394503503, 0.0668068300342269, 0.033332273885795, 0.033332273885795, 0.0334534814824332, 0.0666856224375886, 0.0333704134325707, 0.033315209005018, 0.033315209005018, 0.036271836747067, 0.404983628881114, 0.100242997758416, 0.0333143371362681, 0.0333143371362681, 0.0335434579353297, 0.100013876959354, 0.0334160856749004, 0.0665977912844539, 0.0333281052151391, 0.0332696860693148, 0.0332696860693148, 0.035602651879993, 0.469583651436047, 0.0333546604597588, 0.0333546604597588, 0.0351310395699001, 0.235333664735568, 0.132997427478146, 0.0994761801121919, 0.0331933763620714, 0.0662828037501204, 0.0331543905855766, 0.0331284131645438, 0.0331284131645438, 0.0334591746647036, 0.0664733790448194, 0.0994253937835296, 0.0331156600972852, 0.0331156600972852, 0.0331817163287638, 0.0662527480102788, 0.0331065895417722, 0.0331065895417722, 0.0331409299728323, 0.0662184075792187, 0.0331171440121069, 0.0331012635671118, 0.0331012635671118, 0.0333041674764138, 0.132593017497913, 0.0331172479513072, 0.0331172479513072, 0.033236117024931, 0.0331544840631022, 0.0993196643611872, 0.0331250322385216, 0.0661946321226655, 0.0331042333895905, 0.033090398733075, 0.033090398733075, 0.0331578685247251, 0.0662219348231546, 0.0330943450764097, 0.0330943450764097, 0.0331233839501998, 0.0661928959493644, 0.0331031717428039, 0.0330897242065606, 0.0330897242065606, 0.0345386410734367, 0.333687546959211, 0.0995810842932572, 0.0332602818277515, 0.0663208024655057, 0.0331853266484097, 0.033135475817096, 0.033135475817096, 0.0342068863537849, 0.332759268562643, 0.0663024763360403, 0.0331823132077261, 0.0331201631283143, 0.0331201631283143, 0.0339497425700995, 0.298896150834476, 0.0662158514941083, 0.0331335468570609, 0.0330823046370474, 0.0330823046370474, 0.0337382872727995, 0.199167153815139, 0.033096711558834, 0.0991098496818115, 0.0330596968661419, 0.0660501528156696, 0.0330337207402062, 0.0330164320754635, 0.0330164320754635, 0.033096711558834, 0.0991098496818115, 0.0330596968661419, 0.0660501528156696, 0.0330337207402061, 0.0330164320754635, 0.0330164320754635, 0.0335238634352056, 0.198733795907464, 0.0991160557131153, 0.033070698659828, 0.0660453570532873, 0.0330346483804987, 0.0330107086727886, 0.0330107086727886, 0.0333734895776815, 0.132415866398285, 0.132060495644612, 0.033058817676144, 0.0660135001925425, 0.0329881777759259, 0.0329881777759259, 0.0330204697936901, 0.0659812081747783, 0.0329980693573918, 0.0329831388173865, 0.0329831388173865, 0.0332322826202459, 0.231244079422652, 0.0331573626932116, 0.19808671672944, 0.0330978600915475, 0.164988856637893, 0.0330514538589479, 0.131937402778945, 0.0330161341902396, 0.0989212685887051, 0.0329900908255011, 0.065931177763204, 0.0329717081478354, 0.0329594696153686, 0.0329594696153686, 0.049219840534121, 0.0442144044894478, 0.622965169477472, 0.134654300887825, 0.0341514992652007, 0.0336700021528562, 0.0668327994697676, 0.0334793219457174, 0.0333534775240502, 0.0333534775240502, 0.0336973393800017, 0.033461108745097, 0.0333443534975252, 0.0333443534975252, 0.033461108745097, 0.0333443534975252, 0.0333443534975252, 0.0418255447762887, 0.682183199319774, 0.0336107262692334, 0.0336107262692334, 0.040188894723886, 0.57571336997148, 0.0667108392955394, 0.0331808215981022, 0.0331808215981022, 0.0335066429054619, 0.0332547340606451, 0.0331302839275345, 0.0331302839275345, 0.0332547340606451, 0.0331302839275345, 0.0331302839275345, 0.0388234032404227, 0.405520253139067, 0.0664455217189164, 0.0989902659777992, 0.0329295054813539, 0.0328960813075621, 0.0328960813075621, 0.0329295054813539, 0.0328960813075621, 0.0328960813075621, 0.0330841638740253, 0.0988298520781273, 0.0329018368145627, 0.0329018368145627, 0.0329985806542928, 0.0987331082383971, 0.0329445491176253, 0.0657885591207718, 0.0329068081492381, 0.0328817509715337, 0.0328817509715337, 0.0334116196079887, 0.0661688239788308, 0.065895133940071, 0.0657857969587411, 0.032906539710018, 0.032879257248723, 0.032879257248723, 0.032986515740097, 0.0658152809151543, 0.0328791342435607, 0.0328791342435607, 0.0329282420624337, 0.0657661730962814, 0.0328943411445481, 0.0328718319517333, 0.0328718319517333, 0.033170090017726, 0.164679664859917, 0.0330780398912307, 0.0329517076426448, 0.0986499173260414, 0.032909542434431, 0.0657403748916105, 0.0328800150939334, 0.032860359797677, 0.032860359797677, 0.0329656825463578, 0.032902560714043, 0.0657333817082854, 0.0328756311231184, 0.032857750585167, 0.032857750585167, 0.032902560714043, 0.0657333817082854, 0.0328756311231184, 0.032857750585167, 0.032857750585167, 0.0374770384868721, 0.599304589137827, 0.0366989510358416, 0.496917070890176, 0.0329004814860867, 0.0327880857257226, 0.0327880857257226, 0.0329004814860867, 0.0327880857257226, 0.0327880857257226, 0.036018411895121, 0.232410044916333, 0.196335673751286, 0.0978415075392461, 0.0326593714034844, 0.0326046206446281, 0.0325775154911336, 0.0325775154911336, 0.0326046206446281, 0.0325775154911336, 0.0325775154911336, 0.0330136617146776, 0.163389614489852, 0.0977739050860019, 0.0326244614296583, 0.0651494436563436, 0.0325871376165114, 0.0325623060398322, 0.0325623060398322, 0.0328633582739635, 0.195724071258, 0.0325760900438905, 0.0325760900438905, 0.0327656756827241, 0.162974998747172, 0.0325594868719942, 0.0325594868719942, 0.0326885476405072, 0.162845937978659, 0.0326340325583921, 0.130211905420267, 0.0325927488384898, 0.06509074400318, 0.0325284125785974, 0.0325284125785974, 0.0325580332608029, 0.0650611233209744, 0.0325373102808557, 0.0325238130401187, 0.0325238130401187, 0.0351568241397769, 0.393624977938422, 0.0978054241286657, 0.0326779293699182, 0.0651274947587476, 0.0325921977233945, 0.0325352970353531, 0.0325352970353531, 0.0346890902120009, 0.391765165171537, 0.0325196860130948, 0.032456460670455, 0.032456460670455, 0.0325196860130948, 0.032456460670455, 0.032456460670455, 0.034309654791485, 0.0333069456114031, 0.195153626874022, 0.161671710689911, 0.0322993738882662, 0.0322993738882662, 0.032447894107216, 0.0646722778659995, 0.0968509126049613, 0.0323057809390095, 0.0322791546736518, 0.0322659769923, 0.0322659769923, 0.0322791546736519, 0.0322659769922999, 0.0322659769922999, 0.0323632785849129, 0.129159911886048, 0.0323246350725273, 0.0968352768135205, 0.0322962183017782, 0.0645390585117423, 0.0322761923364492, 0.032262866175293, 0.032262866175293, 0.0330071744033285, 0.226939662551319, 0.0646320021837667, 0.0645458723137841, 0.0322836881935497, 0.0322621841202344, 0.0322621841202344, 0.0323427695825151, 0.0968351049150357, 0.0323031832727936, 0.0645319216422421, 0.0322751609577439, 0.0322567606844982, 0.0322567606844982, 0.0328027358172445, 0.226504947708718, 0.0645588013331726, 0.0322510521897348, 0.0322510521897348, 0.0322998770456797, 0.0645099764772277, 0.0322661800541751, 0.0322437964230526, 0.0322437964230526, 0.0326480403068323, 0.19392503607138, 0.0967417248534136, 0.0322781161625455, 0.0322410564884851, 0.032222552202383, 0.032222552202383, 0.0322410564884851, 0.032222552202383, 0.032222552202383, 0.0325192535552442, 0.258147507369549, 0.0324354170949678, 0.193494906140151, 0.0322171841344303, 0.0322171841344303, 0.0323627595767256, 0.193349330697855, 0.0323085317410806, 0.161040798956775, 0.0322663433133145, 0.0644107184788669, 0.0643637371645934, 0.0321877380703371, 0.0321759990942562, 0.0321759990942562, 0.0322234349183626, 0.064375665903998, 0.0321753548210997, 0.0321753548210997, 0.0321973271902893, 0.0643536935348084, 0.0321819568853583, 0.0321717366494501, 0.0321717366494501, 0.0663355772483993, 0.0327851935602844, 0.194199593142772, 0.129111293112146, 0.0323214921096558, 0.0645388986579754, 0.0322509023445146, 0.0322509023445146, 0.0322831847363074, 0.0645066162661826, 0.0322607651606991, 0.0322458511054835, 0.0322458511054835, 0.0326327359410841, 0.258416972246175, 0.0322611780676587, 0.0322611780676587, 0.0325331105282313, 0.258145039785602, 0.0324544101185645, 0.0968276626385371, 0.128862967028501, 0.03224437170852, 0.0966185953199806, 0.0322208856879889, 0.0643977096319917, 0.0322044205817622, 0.0321932890502295, 0.0321932890502295, 0.0323561570968401, 0.193334472570198, 0.0323073802245886, 0.0644527910416568, 0.0965743013039523, 0.0322049703338378, 0.0643693309701144, 0.0321897440214228, 0.0321795869486916, 0.0321795869486916, 0.0322488082982109, 0.128778284047398, 0.0322211943816908, 0.0965570896657074, 0.0322008135554876, 0.0321825922356856, 0.0321736838745343, 0.0321736838745343, 0.0321825922356856, 0.0321736838745343, 0.0321736838745343, 0.0977661335251696, 0.0324288988591102, 0.129155651327545, 0.096745396103377, 0.0322656355770511, 0.0322449552924263, 0.0322348052338997, 0.0322348052338997, 0.0322449552924263, 0.0322348052338997, 0.0322348052338997, 0.0323595251371313, 0.193541522293791, 0.0323187380940504, 0.128991023475239, 0.0322317607245018, 0.0322317607245018, 0.0322829911453707, 0.12893979305437, 0.0322579686650949, 0.096681824389275, 0.0322391519922035, 0.0644426723970716, 0.0322258148629122, 0.0322168575341594, 0.0322168575341594, 0.0647573305441683, 0.1613250101675, 0.0322476055783646, 0.0322476055783646, 0.0323355850296589, 0.129000971944401, 0.0322360587718044, 0.0322360587718044, 0.0323008621078318, 0.0322551455280176, 0.0644597667670972, 0.0322212563132586, 0.0322212563132586, 0.0322367451852314, 0.0644442778951245, 0.0322257685871638, 0.0322185093079607, 0.0322185093079607, 0.0322565899416391, 0.0644587280747614, 0.032220850591973, 0.032220850591973, 0.0322379815797553, 0.0322242394577704, 0.0322173576292087, 0.0322173576292087, 0.0322242394577704, 0.0322173576292087, 0.0322173576292087, 0.431221198201524, 0.337117026002302, 0.0334956506509189, 0.0334956506509189, 0.035393461700969, 0.101759394252467, 0.0670480547177123, 0.0666798835143864, 0.0332690768972138, 0.0664628055704725, 0.0332408035463199, 0.0332220020241526, 0.0332220020241526, 0.0332734076216484, 0.0332379759608894, 0.0332204988851485, 0.0332204988851485, 0.0332379759608894, 0.0332204988851485, 0.0332204988851485, 0.0333841006577371, 0.0665575642471301, 0.0664701010772055, 0.0332459666250396, 0.0332241344521659, 0.0332241344521659, 0.0333059200539609, 0.0997217452703747, 0.0332656378514864, 0.0664561074188883, 0.033237447111729, 0.0332186603071593, 0.0332186603071593, 0.0335903618348942, 0.166604644984885, 0.0332648138800062, 0.0332648138800062, 0.0334705682847145, 0.166398890580176, 0.0333883609045305, 0.0333075956252234, 0.0664843072878076, 0.0332186267626148, 0.0332186267626148, 0.0332593185799993, 0.0664436154704231, 0.0332311750767805, 0.0332124403936426, 0.0332124403936426, 0.0665502243399363, 0.0664603053357095, 0.0332413741272138, 0.0332189312084957, 0.0332189312084957, 0.0345957269695685, 0.0339960278859806, 0.033616704770672, 0.23301075532603, 0.033492230553081, 0.166305742639903, 0.0332127821330463, 0.0332127821330463, 0.0333889652041823, 0.13293344440431, 0.033196115164457, 0.033196115164457, 0.0333102180024322, 0.099635870601665, 0.03318347096467, 0.03318347096467, 0.0332508626546078, 0.0995684789117272, 0.0332130469279653, 0.0663554319837619, 0.0331865576747813, 0.0331688743089806, 0.0331688743089806, 0.0670660561906861, 0.133137088992633, 0.0332264942489915, 0.0331978206643915, 0.0331978206643915, 0.0332264942489915, 0.0331978206643915, 0.0331978206643915, 0.0334098216156472, 0.166151582290369, 0.0333364411071866, 0.0664516093550761, 0.0331904972078906, 0.033173034620216, 0.033173034620216, 0.0331904972078906, 0.033173034620216, 0.033173034620216, 0.0332631990214736, 0.0332070842442788, 0.0331793230715155, 0.0331655348459147, 0.0331655348459147, 0.0331793230715155, 0.0331655348459147, 0.0331655348459147, 0.0332070842442787, 0.0331793230715156, 0.0331655348459147, 0.0331655348459147, 0.0331793230715156, 0.0331655348459147, 0.0331655348459147, 0.067480901928543, 0.23314258605414, 0.0336064253815275, 0.0333790199310229, 0.132953358626517, 0.0332037821150732, 0.0332037821150732, 0.0333059873229505, 0.132851153418639, 0.0332566135988614, 0.0995945398197778, 0.0332206334408526, 0.0663739063789252, 0.0331953688330654, 0.0331785375458598, 0.0331785375458598, 0.0333893382166061, 0.0333025858797682, 0.132844236576238, 0.0332541216455926, 0.0995901149306458, 0.0332187743786884, 0.0663713405519574, 0.033193937858785, 0.0331774026931724, 0.0331774026931724, 0.0997508888409092, 0.0332083677926078, 0.0331875658224896, 0.0331875658224896, 0.0332083677926079, 0.0331875658224896, 0.0331875658224896), Nnode = 378L, tip.label = c("Letrouitia_domingensis_1_55", "Letrouitia_transgressa_29", "Letrouitia_vulpina_72", "Letrouitia_subvulpina_44", "Letrouitia_parabola_11", "Letrouitia_flavidula_35", "Brigantiaea_sorediata_4962", "Brigantiaea_fuscolutea_65", "Brigantiaea_cf_leucoxantha_71", "Letrouitia_sp_206", "Brigantiaea_tricolor_26", "Brigantiaea_leucoxantha_17", "Brigantiaea_cf_tricolor_70", "Lecania_sulphureofusca_30", "Megaloblastenia_marginiflexa_69", "Megalospora_pruinata_43", "Megalospora_admixta_42", "Megalospora_sulphurata_73", "Megalospora_coccodes_94", "Megalospora_coccodes_25", "Megalospora_isidiata_93", "Megalospora_tuberculosa_gr_1_52", "Megalospora_tuberculosa_107", "Fauriea_chujaensis", "Fauriea_orientochinensis", "Caloplaca_proteus_13706", "Upretia_amarkantakana", "Ioplaca_pindarensis_37", "Ioplaca_pindarensis_199", "Loekoesia_austrocoreana", "Jasonhuria_bogilana", "Gyalolechia_aurea", "Fulgensia_canariensis_3593", "Fulgensia_bracteata_ssp_bracteata_AF277666", "Fulgensia_bracteata_4844", "Fulgensia_klementii_7480_254", "Fulgensia_klementii_7350_253", "Fulgensia_desertorum_395", "Fulgensia_poeltii_400", "Fulgensia_fulgens_39", "Fulgensia_desertorum_1_395", "Caloplaca_gloriae_1_251", "Gyalolechia_gomerana", "Caloplaca_gloriae_59", "Caloplaca_gloriae_251", "Caloplaca_cinnamomea_24", "Blastenia_ferruginea", "Caloplaca_crenularia_19", "Caloplaca_cf_amniospila_100", "Blastenia_circumpolaris", "Gyalolechia_stantonii", "Caloplaca_aff_flavorubescens_164", "Caloplaca_aff_flavorubescens_160", "Caloplaca_flavorubescens_2090", "Gyalolechia_flavovirescens", "Caloplaca_flavorubescens_We6140", "Mikhtomia_gordejevii", "Mikhtomia_yeosuensis", "Mikhtomia_multicolor", "Caloplaca_gr_citrina_232", "Huneckia_pollinii", "Caloplaca_lecapsulata", "Caloplaca_lecanorocarpa", "Eilifdahlia_wirthii", "Eilifdahlia_dahlii", "Franwilsia_kilcundaensis", "Franwilsia_bastowii", "Franwilsia_renatae", "Caloplaca_pellodella_150", "Caloplaca_furax_46", "Rufoplaca_tristiuscula", "Caloplaca_scotoplaca_40", "Huea_cerussata_196", "Huea_coralligera_195", "Yoshimuria_galbina", "Yoshimuria_spodoplaca", "Caloplaca_aff_peliophylla_152", "Caloplaca_carphinea_51", "Caloplaca_scoriophila_47", "Caloplaca_carphinea_2_201", "Caloplaca_aff_submergenda_107", "Caloplaca_aff_submergenda_109", "Caloplaca_teicholyta_13695", "Caloplaca_albolutescens", "Caloplaca_aetnensis_236", "Caloplaca_erythrocarpa_13691", "Caloplaca_teicholyta_2_13695", "Caloplaca_submergenda_107", "Caloplaca_submergenda_109", "Caloplaca_chalybaea_38", "Caloplaca_transcaspica", "Caloplacamicrostepposa", "Pyrenodesmia_erodens", "Caloplaca_variabilis_189", "Caloplaca_micromontana", "Caloplaca_sp_41", "Caloplaca_micromarina", "Pyrenodesmia_alociza", "Olegblumia_demissa", "Bryoplaca_sinapisperma", "Bryoplaca_tetraspora", "Bryoplaca_jungermanniae", "Seirophora_lacunosa_10", "Seirophora_californica_153", "Seirophora_californica_80", "Caloplaca_xantholyta_32", "Caloplaca_cirrochroa_2_13711", "Caloplaca_proteus_2_13706", "Caloplaca_thracopontica_56", "Caloplaca_stillicidiorum_405", "Caloplaca_cerina_16", "Caloplaca_stillicidiorum_217", "Caloplaca_isidiigera_58", "Caloplaca_chlorina_57", "Caloplaca_chlorina_191", "Caloplaca_chlorina_2055", "Seirophora_blumii", "Seirophora_contortuplicatus_27_EU639614", "Seirophora_contortuplicata_27", "Seirophora_contortuplicata_197", "Caloplaca_velana_vardolomiticola_2_409", "Fulgensia_australis_BCN", "Caloplaca_paulii_183", "Caloplaca_velana_409", "Caloplaca_cancaraxiticola_375", "Caloplaca_velana_192", "Caloplaca_aurantia_13326", "Caloplaca_aegaea_248", "Caloplaca_thallincola_401", "Caloplaca_aegaea_2_248", "Caloplaca_aurantia_1_13326", "Caloplaca_flavescens_4_186", "Caloplaca_thallincola_22", "Caloplaca_thallincola_1_401", "Xanthomendoza_novozelandica_50t1", "Xanthomendoza_weberi_202", "Xanthomendoza_weberi_201", "Xanthomendoza_fulva_85", "Shackletonia_hertelii", "Shackletonia_buelliae", "Shackletonia_cryodesertorum", "Shackletonia_sauronii", "Xanthopeltis_rupicola_246", "Caloplaca_orthoclada_252", "Caloplaca_luteoalba_41", "Cerothallia_yorkensis", "Gondwania_sp_18", "Gondwania_sejongensis", "Gondwania_regalis", "Gondwania_cribrosa", "Pachypeltis_invadens", "Pachypeltis_intrudens", "Pachypeltis_sp_23", "Pachypeltis_sp_24", "Parvoplaca_tiroliensis", "Parvoplaca_athallina", "Parvoplaca_servitiana", "Parvoplaca_suspiciosa", "Pachypeltis_sp_26", "Parvoplaca_nigroblastidiata", "Caloplaca_trachyphylla_385", "Xanthomendoza_mendozae_20", "Xanthomendoza_mendozae_203", "Xanthomendoza_mendozae_174", "Xanthomendoza_fallax_33", "Oxneria_sp", "Xanthomendoza_ulophyllodes_78", "Oxneria_alfredii", "Xanthomendoza_hasseana_5_120", "Xanthomendoza_montana_84", "Xanthomendoza_sogdiana", "Xanthomendoza_borealis_77", "Xanthomendoza_borealis_FNM029", "Xanthomendoza_borealis_029_3451", "Xanthomendoza_galericulata", "Xanthomendoza_oregana_173", "Xanthomendoza_fulva_98", "Xanthomendoza_poeltii_7", "Gallowayella_coppinsii", "Caloplaca_ferruginea_230", "Caloplaca_aff_arnoldii_241", "Caloplaca_inconnexa_ssp_nesodes_106", "Caloplaca_squamosa_151", "Caloplaca_cf_inconnexa_ssp_nesodes_106", "Charcotiana_antarctica", "Caloplaca_zeorina", "Caloplaca_scrobiculata_407", "Amundsenia_approximata", "Amundsenia_austrocontinentalis", "Caloplaca_sp_218", "Caloplaca_marmorata_416", "Caloplaca_ochracea_21", "Caloplaca_crenulatella_111", "Caloplaca_squamosa_sl_49", "Caloplaca_sp_225", "Austroplaca_sp_10", "Austroplaca_sp_9", "Caloplaca_millegrana_200", "Austroplaca_sp_7", "Austroplaca_darbishirei", "Austroplaca_soropelta", "Austroplaca_lucens", "Austroplaca_hookeri", "Austroplaca_cirrochrooides", "Solitaria_chrysopthalma", "Caloplaca_coralloides_79", "Orientophila_sp_21", "Orientophila_sp_22", "Coppinsiella_ulcerosa", "Coppinsiella_substerilis", "Caloplaca_substerilis_subsp_orbicularis", "Coppinsiella_orbicularis", "Caloplaca_gr_citrina_240", "Caloplaca_maritima_243b", "Caloplaca_granulosa_13702", "Caloplaca_sol", "Caloplaca_maritima_1_248b", "Caloplaca_marina_sspmarina_331", "Caloplaca_microthallina_454", "Caloplaca_coronata_48", "Caloplaca_coronata_394", "Caloplaca_oasis", "Caloplaca_polycarpa_399", "Flavoplaca_mereschkowskiana", "Caloplaca_skii", "Caloplaca_inconnexa_13375", "Caloplaca_ignea_360", "Athallia_cerinelloides", "Athallia_holocarpa", "Caloplaca_alcarum_2_459", "Caloplaca_scopularis_374", "Caloplaca_cf_crenulatella_108", "Caloplaca_aff_arenaria_101", "Caloplaca_bolacina_414", "Caloplaca_ignea_104", "Caloplaca_ignea_1_360", "Caloplaca_cf_pyracea_99", "Caloplaca_cf_boulyi_114", "Caloplaca_pyracea_99", "Caloplaca_sp_148", "Caloplaca_gr_cerina_154", "Caloplaca_verruculifera_23", "Caloplaca_impolita_105", "Caloplaca_sp_163", "Xanthoria_cf_concinna_97", "Xanthoria_polycarpa_4", "Xanthoria_tenax_96", "Xanthomendoza_fulva_251", "Xanthoria_candelaria_2", "Massjukiella_alaskana", "Massjukiella_ucrainica", "Xanthoria_polycarpa_4_Hon215", "Massjukiella_kaernefeltii", "Xanthoria_candelaria_2_8444", "Xanthoria_resendei_2_233b", "Xanthoria_aureola_9", "Xanthoria_calcicola_3_U257", "Xanthoria_calcicola_3", "Xanthoria_parietina_8", "Xanthoria_sp_76", "Caloplaca_scopularis_4820_374", "Caloplaca_marina_4819_331", "Xanthodactylon_flammea_95", "Xanthoria_ligulata_AF5628", "Xanthoria_ligulata_5628_011", "Jackelixia_filsonii", "Jackelixia_streimannii", "Jackelixia_elixii", "Xanthoria_sp_249", "Xanthoria_karrooensis_AF5627", "Ovealmbornia_reginae", "Ovealmbornia_volkmarwirthii", "Dufourea_bonae_spei", "Langeottia_ottolangei", "Xanthoria_karrooensis_5627_066", "Xanthodactylon_inflata", "Xanthoria_turbinata_FNM119", "Xanthodactylon_flammeum", "Xanthoria_flammea", "Zeroviella_ussurica", "Xanthoria_sorediata_1_367", "Xanthoria_sorediata_AF5635", "Zeroviella_esfahanensis", "Xanthoria_elegans_1_192", "Zeroviella_mandschurica", "Zeroviella_laxa", "Zeroviella_coreana", "Zeroviella_papillifera", "Xanthoria_elegans_13", "Xanthoria_sorediata_367", "Xanthoria_sorediata_5635_046", "Xanthoria_turbinata_119", "Seawardiella_tasmaniensis", "Caloplaca_arnoldii_ssp_oblit_5", "Caloplaca_decipiens_2_342b", "Caloplaca_schistidii_245", "Calogaya_qinghaiensis", "Calogaya_biatorina_subsp__asiatica", "Calogaya_xanthoriella", "Calogaya_altynis", "Calogaya_orientalis", "Calogaya_haloxylonis", "Calogaya_xinjiangis", "Caloplaca_decipiens_2377_342b", "Calogaya_mogoltanica", "Lazarenkoella_zoroasteriorum", "Lazarenkoella_polycarpoides", "Caloplaca_chilensis_68", "Hosseusiella_gallowayiana", "Teloschistes_hypoglaucus", "Teloschistes_hosseusianus_50", "Teloschistes_cf_nodulifer_216", "Teloschistes_cf_chrysophthalmus_248", "Teloschistes_chrysophthalmus_2_13687", "Teloschistes_chrysophtalmus_06_1", "Teloschistes_cf_chrysophtalmus_147", "Teloschistes_flavicans_103", "Teloschistes_flavicans_102", "Teloschistes_exilis_12", "Teloschistes_siberianus_2_423", "Xanthomendoza_sp_243", "Teloschistes_siberianus_423", "Teloschistes_fasciculatus_427", "Tassiloa_digitaurea", "Caloplaca_sp_221", "Caloplaca_gr_arenaria_239", "Tayloriella_erythrosticta", "Caloplaca_microphyllina_115", "Villophora_isidioclada", "Villophora_sp_50", "Villophora_sp_48", "Josefpoeltia_parva_184", "Josefpoeltia_sorediosa", "Josefpoeltia_parva_447t2", "Caloplaca_elegantissima_75", "Kaernefia_gilfillaniorum", "Kaernefia_albocrenulata", "Caloplaca_cinnabarina_149", "Brownliella_kobeana", "Brownliella_montisfracti", "Brownliella_aequata", "Caloplaca_aff_maritima_110", "Filsoniana_rexfilsonii", "Filsoniana_kiamae", "Thelliana_pseudokiamae", "Scutaria_andina", "Xanthoria_andina_31", "Catenarina_vivasiana", "Catenarina_desolata", "Caloplaca_cf_chrysophthalma_157", "Caloplaca_sp_167", "Caloplaca_sp_171", "Caloplaca_decipioides_188", "Caloplaca_sp_234", "Caloplaca_brouardii_159", "Caloplaca_sp_228", "Caloplaca_sp_236", "Caloplaca_sp_220", "Wetmoreana_sp_52", "Caloplaca_santessoniana_242", "Caloplaca_sp_237", "Caloplaca_sp_238", "Rehmanniella_wirthii", "Teloschistopsis_bonae_spei", "Teloschistopsis_eudoxa", "Caloplaca_cf_luteoalba_155", "Haloplaca_sp_6", "Caloplaca_luteoalba_155", "Haloplaca_suaedae", "Caloplaca_syvashica", "Caloplaca_sp_244", "Sirenophila_gintarasii", "Caloplaca_sp_245", "Tarasginia_whinrayi", "Caloplaca_eos_190", "Sirenophila_gallowayii", "Sirenophila_jackelixii", "Sirenophila_ovis_atra", "Sirenophila_bermaguiana")), class = c("chronos", "phylo"), order = "cladewise", call = chronos(phy = ASTRAL_tree), ploglik = -880.649170886665, rates = c(29.2561306457455, 29.2537444395667, 29.2533673654652, 29.2533845928844, 29.2533845928844, 29.2534783006907, 29.2535446916122, 29.2536173526435, 29.2536173526435, 29.2535446916122, 29.2536173526435, 29.2536173526435, 29.2529609644993, 29.2520276172543, 29.2519983810817, 29.2519983810817, 29.2519681757668, 29.2517682467232, 29.2518111675045, 29.2518111675045, 29.2518382785342, 29.2518673251069, 29.2519521971173, 29.2520373816894, 29.2520373816894, 29.3742098247393, 29.339917738941, 29.3379563191786, 29.3379874965092, 29.3371238038981, 29.3380127907695, 29.337905863672, 29.3379892765655, 29.3379892765655, 29.338823208513, 29.3391077083061, 29.3392301422908, 29.3392301422908, 29.3397018427716, 29.3399875629503, 29.3404217422992, 29.3406970611309, 29.3408592978301, 29.3410286834379, 29.3410286834379, 29.4920979222618, 29.5300915137394, 29.5278234044734, 29.5282865532472, 29.5284378802822, 29.5284378802822, 29.5289633079942, 29.5293314292525, 29.5298003555397, 29.5301160544227, 29.5302817189811, 29.5304610508877, 29.5304610508877, 29.5859178400766, 29.6022986559251, 29.6034715237121, 29.6206171914044, 29.627871518677, 29.6290324382481, 29.6338476647589, 29.6351167024484, 29.6353440711657, 29.6353440711657, 29.6384455295798, 29.640669802056, 29.6413433916513, 29.6420266022496, 29.6424840208617, 29.6427134722145, 29.6429442157885, 29.6429442157885, 29.640669802056, 29.6413433916513, 29.6420266022496, 29.6424840208617, 29.6427134722145, 29.6429442157885, 29.6429442157885, 29.631906976987, 29.6344490588411, 29.635081277427, 29.6357181929883, 29.6361548771166, 29.6363655211617, 29.6365857186781, 29.6365857186781, 29.6406871942611, 29.6441030613588, 29.6449664291057, 29.6463244176998, 29.6469951321518, 29.6476857575317, 29.6481445778495, 29.6483793110785, 29.6486118674367, 29.6486118674367, 29.6460052833404, 29.6477217775369, 29.6481685594067, 29.6483906854431, 29.6486192521468, 29.6486192521468, 29.6494803415846, 29.6503518720806, 29.6519170090031, 29.6527984012968, 29.6530212940558, 29.6530212940558, 29.6532839094354, 29.6537436652392, 29.6539811783052, 29.6542153881626, 29.6542153881626, 29.6277943758016, 29.6304193290376, 29.6322039814341, 29.6327476114872, 29.6333609790101, 29.6337608337389, 29.6339741267975, 29.6341894742184, 29.6341894742184, 29.6324305024738, 29.6331804697087, 29.6333807497163, 29.6333807497163, 29.6336202906968, 29.6340273814035, 29.634256818911, 29.6344764871593, 29.6344764871593, 29.6687257933029, 29.6709847413882, 29.6717972518233, 29.6719900421249, 29.6719900421249, 29.6727106045001, 29.6732494778624, 29.6738238571136, 29.6742163499989, 29.6744085201304, 29.6746151464724, 29.6746151464724, 29.7086774078129, 29.7098159407307, 29.709976818166, 29.709976818166, 29.7484597993692, 29.7616546050224, 29.7643453756466, 29.765003924601, 29.7656856127866, 29.7661380832507, 29.7663698373282, 29.766600367348, 29.766600367348, 29.7722194041431, 29.7761635733153, 29.7772928241198, 29.777524473079, 29.777524473079, 29.7786311304758, 29.7795462667953, 29.7797757630045, 29.7797757630045, 29.7799916380621, 29.7804560183775, 29.7806766576197, 29.7809066317074, 29.7809066317074, 29.7787772715006, 29.780119065324, 29.780355389384, 29.780355389384, 29.7838523009082, 29.786178350088, 29.7868765916569, 29.7875902713863, 29.7880652976126, 29.7883033457621, 29.7885464714657, 29.7885464714657, 29.7864300092662, 29.787376992391, 29.7876171550325, 29.7876171550325, 29.7878506732169, 29.7883281009867, 29.7885693118597, 29.7888134220581, 29.7888134220581, 29.7758025658709, 29.7787034692373, 29.779287264756, 29.7799543843352, 29.7803792301355, 29.7806157216845, 29.7808442789175, 29.7808442789175, 29.8007206723024, 29.8031060197041, 29.8035062410402, 29.8037100691172, 29.8039223970721, 29.8039223970721, 29.8235791551854, 29.8260489680171, 29.826465691108, 29.8266784678134, 29.82689943238, 29.82689943238, 29.8441775398218, 29.849641387498, 29.8519162334536, 29.8526044476987, 29.8533021238096, 29.8537711251893, 29.8540049498989, 29.8542419309202, 29.8542419309202, 29.8519162334536, 29.8526044476988, 29.8533021238096, 29.8537711251893, 29.8540049498989, 29.8542419309202, 29.8542419309202, 29.8594293677587, 29.8625591433958, 29.8632263369566, 29.8639251676004, 29.8643853277473, 29.8646227882653, 29.8648602226643, 29.8648602226643, 29.8715719049267, 29.8757876802012, 29.8766991212575, 29.8783587863747, 29.8793062112193, 29.8795489614614, 29.8795489614614, 29.8797748176589, 29.8802498947744, 29.8804894759889, 29.8807311599105, 29.8807311599105, 29.879451538388, 29.8809565562303, 29.8857095327055, 29.887038510197, 29.8904856591747, 29.8916239637315, 29.8939485861872, 29.8948805451669, 29.8962876578638, 29.8969964815806, 29.8977040345618, 29.8981801630359, 29.8984152579349, 29.8986541466678, 29.8986541466678, 29.5879346421491, 29.6637565993017, 29.6574183231928, 29.6575235179369, 29.6589915649738, 29.6597576422555, 29.660050862185, 29.6602116722892, 29.6603853567701, 29.6603853567701, 29.6600190404875, 29.6605277703808, 29.6607177612253, 29.6607177612253, 29.6605277703808, 29.6607177612253, 29.6607177612253, 29.7511681957566, 29.7462491174058, 29.7462493688596, 29.7462493688596, 29.8476100574771, 29.8459754314046, 29.8464392529176, 29.8465968099937, 29.8465968099937, 29.8469382423487, 29.8474237483319, 29.8476064223314, 29.8476064223314, 29.8474237483319, 29.8476064223315, 29.8476064223315, 29.9490300116793, 29.9630853814267, 29.9686513892885, 29.9705932237542, 29.9712853452202, 29.9715211045739, 29.9715211045739, 29.9712853452202, 29.9715211045739, 29.9715211045739, 29.972130693986, 29.9732390485611, 29.9734732256319, 29.9734732256319, 29.9743586607406, 29.9750360799178, 29.9757302627207, 29.9761937960417, 29.9764281128882, 29.9766632638719, 29.9766632638719, 29.974086298776, 29.9784577949877, 29.9800437709188, 29.9805072443252, 29.9807551238729, 29.9809946023358, 29.9809946023358, 29.9809686751983, 29.9818857133897, 29.9821209870398, 29.9821209870398, 29.9823782911414, 29.9828523636428, 29.9831017423377, 29.9833473777239, 29.9833473777239, 29.9807382509255, 29.9817821808558, 29.9862539819762, 29.9885800737763, 29.9892751964513, 29.9900111124205, 29.9904897784281, 29.990742775363, 29.9909923400063, 29.9909923400063, 29.9893095796375, 29.9907403012275, 29.9912186819349, 29.9914682452709, 29.9917145299206, 29.9917145299206, 29.9907403012275, 29.9912186819349, 29.9914682452709, 29.9917145299205, 29.9917145299205, 30.0391130146327, 30.0390737922281, 30.131325247646, 30.1329236728049, 30.1335001537642, 30.1337118952626, 30.1337118952626, 30.1335001537642, 30.1337118952626, 30.1337118952626, 30.2236867017997, 30.238325596393, 30.2416878281619, 30.2423682556023, 30.2433350597663, 30.244056761146, 30.2443016723216, 30.2443016723216, 30.244056761146, 30.2443016723216, 30.2443016723216, 30.2500605114972, 30.253072971835, 30.2537623702578, 30.2544557055118, 30.2549282971706, 30.2551572613974, 30.255396126809, 30.255396126809, 30.2587600160907, 30.2605000931777, 30.2607315016056, 30.2607315016056, 30.2656312489839, 30.2672327289615, 30.2674775129272, 30.2674775129272, 30.2707621968665, 30.2719236778028, 30.274555320409, 30.2755081106942, 30.2771974519329, 30.2781671210756, 30.2784088898536, 30.2784088898536, 30.2786573286743, 30.2791524116413, 30.2793948339376, 30.2796445632494, 30.2796445632494, 30.3028712059076, 30.3058981468999, 30.3064938433235, 30.3071611872442, 30.3075959013836, 30.3078279685246, 30.3080612476362, 30.3080612476362, 30.3801028753702, 30.3830073576079, 30.3836604811, 30.3838887184009, 30.3838887184009, 30.3836604811, 30.3838887184009, 30.3838887184009, 30.4553165214598, 30.4886952664966, 30.4979003305826, 30.4995087423465, 30.4997491216457, 30.4997491216457, 30.5047103395677, 30.5076928304641, 30.5084360031219, 30.5094883475805, 30.5102656457936, 30.5105274162667, 30.5105274162667, 30.5102656457936, 30.5105274162667, 30.5105274162667, 30.5083660747034, 30.5093391603654, 30.5108451224647, 30.5115885707457, 30.5123551685104, 30.5128597541058, 30.5131217037195, 30.5133782080253, 30.5133782080253, 30.5131223192142, 30.5184793482326, 30.5201887431211, 30.5206847379626, 30.52094826526, 30.5212041716998, 30.5212041716998, 30.5209109301357, 30.5216428405939, 30.522399238756, 30.522898683436, 30.5231558920127, 30.5234107318368, 30.5234107318368, 30.5323072414391, 30.5361172789112, 30.5370680343514, 30.537310155387, 30.537310155387, 30.5376098333798, 30.5381074966611, 30.5383785226747, 30.5386407070101, 30.5386407070101, 30.5477056108985, 30.5514322987944, 30.5521587454219, 30.553195233526, 30.5539610661915, 30.5542202187955, 30.5542202187955, 30.5539610661915, 30.5542202187955, 30.5542202187955, 30.5593351155742, 30.5611455126519, 30.5690614367611, 30.5709184496917, 30.571154365998, 30.571154365998, 30.57679356222, 30.5782249565346, 30.5829345971498, 30.5841515204277, 30.5876642014155, 30.5894283787103, 30.5899344833131, 30.5901952305321, 30.5904534464635, 30.5904534464635, 30.5904205416488, 30.591424105298, 30.5916809566876, 30.5916809566876, 30.5919403507383, 30.5924497395807, 30.5927073104633, 30.5929626528115, 30.5929626528115, 30.4978875234903, 30.5199077649215, 30.5248010943371, 30.5257687173478, 30.5275451346961, 30.5285570051253, 30.528819563208, 30.528819563208, 30.5290548657481, 30.5295568844076, 30.5298161482832, 30.5300708665485, 30.5300708665485, 30.5370424394961, 30.5392889404132, 30.5395271589386, 30.5395271589386, 30.551874470877, 30.553718355846, 30.5647579698174, 30.5689312963988, 30.5699285505072, 30.5714538815868, 30.5722114865968, 30.5729822615466, 30.5734926884892, 30.5737509475477, 30.5740108442609, 30.5740108442609, 30.5733332362382, 30.5747894431604, 30.5802761530952, 30.5830231807287, 30.5837831386226, 30.5845412899703, 30.5850506795185, 30.5853018627583, 30.5855580061498, 30.5855580061498, 30.5842701984281, 30.585273645035, 30.5870361398742, 30.5877971914125, 30.5888047982581, 30.5895678742173, 30.5898231270817, 30.5898231270817, 30.5895678742173, 30.5898231270817, 30.5898231270817, 30.5188190639739, 30.5295663893815, 30.5330318851375, 30.533786392343, 30.5348115813066, 30.5355817799475, 30.5358390964159, 30.5358390964159, 30.5355817799475, 30.5358390964159, 30.5358390964159, 30.5366908258803, 30.5381603151524, 30.542146328184, 30.54365018752, 30.5439070278504, 30.5439070278504, 30.5458859128041, 30.5468908127152, 30.5483932005939, 30.5491525722762, 30.5499020012092, 30.5504114373566, 30.5506577972654, 30.5509124619877, 30.5509124619877, 30.528724022572, 30.5304604933809, 30.5307161373017, 30.5307161373017, 30.5365198347515, 30.5380245953662, 30.5382779166993, 30.5382779166993, 30.5426041246993, 30.5454219620897, 30.5464512220774, 30.5467103415918, 30.5467103415918, 30.546967798534, 30.5474831964246, 30.5477438200896, 30.5480068685931, 30.5480068685931, 30.5456478856182, 30.5466710073894, 30.546927355813, 30.546927355813, 30.5474343943125, 30.548202051625, 30.5484588574323, 30.5484588574323, 30.548202051625, 30.5484588574323, 30.5484588574323, 29.6156650836703, 29.616174898574, 29.6162992472703, 29.6162992472703, 29.6559034913459, 29.6696744945794, 29.6770516837748, 29.6803520739921, 29.6816937205613, 29.6821499835958, 29.6823728390885, 29.6826021764149, 29.6826021764149, 29.6819578557666, 29.6826567240492, 29.682892225643, 29.682892225643, 29.6826567240492, 29.682892225643, 29.682892225643, 29.6809554182484, 29.6825020295708, 29.682954434658, 29.6831842541141, 29.6834154668324, 29.6834154668324, 29.6831619278357, 29.6838311792621, 29.6845082596127, 29.6849647851854, 29.685191475711, 29.6854215581096, 29.6854215581096, 29.6763947891416, 29.6777920036792, 29.6780167689363, 29.6780167689363, 29.6816594096155, 29.6826881268497, 29.6857830713988, 29.6882077991359, 29.6891027391449, 29.6893323315755, 29.6893323315755, 29.68955173368, 29.6900069545424, 29.6902310304588, 29.6904601501691, 29.6904601501691, 29.6873322565043, 29.6877857836276, 29.6880176409753, 29.6882492377944, 29.6882492377944, 29.6832084012876, 29.6994326313984, 29.7071929453298, 29.7084953291154, 29.7136265626485, 29.7150540314424, 29.7152769411304, 29.7152769411304, 29.7185544620528, 29.7198282524435, 29.7200523179195, 29.7200523179195, 29.7220782964708, 29.7231809406942, 29.7234098341922, 29.7234098341922, 29.724333935895, 29.725010877913, 29.7257135563615, 29.7261769328011, 29.7264152091667, 29.7266529007249, 29.7266529007249, 29.7080663241482, 29.7100659153155, 29.7106981017628, 29.7109128636044, 29.7109128636044, 29.7106981017628, 29.7109128636044, 29.7109128636044, 29.7145802982556, 29.7156278378035, 29.7199295577964, 29.7217161263063, 29.7224012940347, 29.7226329717689, 29.7226329717689, 29.7224012940348, 29.7226329717689, 29.7226329717689, 29.723343155058, 29.7249557158572, 29.7256553840606, 29.7258905580427, 29.7258905580427, 29.7256553840606, 29.7258905580427, 29.7258905580427, 29.7249557158573, 29.7256553840606, 29.7258905580427, 29.7258905580427, 29.7256553840606, 29.7258905580427, 29.7258905580427, 29.6947446022584, 29.6960322781435, 29.7050601275736, 29.7098413853064, 29.7111337601279, 29.7113602285571, 29.7113602285571, 29.7131868956968, 29.7140701798869, 29.7154697302095, 29.7161552525703, 29.7168701629684, 29.7173403987726, 29.7175850351943, 29.7178264669572, 29.7178264669572, 29.7105701769641, 29.7139266301297, 29.7148099591082, 29.7162198176563, 29.7169024472611, 29.7176268698953, 29.7180981787231, 29.7183480325056, 29.7185930376482, 29.7185930376482, 29.7125868398426, 29.7132898053418, 29.7135277779708, 29.7135277779708, 29.7132898053417, 29.7135277779708, 29.7135277779708), message = "relative convergence (4)", PHIIC = list( logLik = -880.345483810127, k = 1133L, lambda = 1, PHIIC = 4026.88934104377))

theo-llewellyn commented 5 years ago

Sorry for the massively long message! Haha.

On inspecting the dendrograms produced by as.dendrogram I think something may going on at this stage as they have 0 members. Is it possible that the way ASTRAL adds branch annotations with square brackets could be affecting how the tree is converted into a dendrogram?

The dendrograms and all other dendextend functions work beautifully when I feed them a trees from other programmes.

dezordi commented 5 years ago

Sorry for the massively long message! Haha.

On inspecting the dendrograms produced by as.dendrogram I think something may going on at this stage as they have 0 members. Is it possible that the way ASTRAL adds branch annotations with square brackets could be affecting how the tree is converted into a dendrogram?

The dendrograms and all other dendextend functions work beautifully when I feed them a trees from other programmes.

Hi theo, I get that error when I try to insert a Bayesian tree with several unresolved clades, so the final tree had several clades with branch length equal to 0, I just resolve this when I'm re-run the phylogenetic analysis and that "unresolved clades" are defined.

This occur because that package is designed to work with hierarchical clusters, and hierarchical cluster never has branch length = 0.

I hope that help u.

Best,

theo-llewellyn commented 5 years ago

Hi dezordi, Ah that makes sense, I had to collapse poorly supported branches in my gene trees before producing my ASTRAL tree so that will have lead to unresolved in my tree too. Thanks for the advice! And thanks again @talgalili for dendextend, its a great package and it has been so useful in my analysis. Will let you know when the work is done :)