Journal article Open Access

Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds

Del Cortona, Andrea; Jackson, Christopher J.; Bucchini, François; Van Bel, Michiel; D'hondt, Sofie; Škaloud, Pavel; Delwiche, Charles F.; Knoll, Andrew H.; Raven, John A.; Heroen Verbruggen; Vandepoele, Klaas; De Clerck, Olivier; Leliaert, Frederik

Gene and protein sequences, corresponding sequence alignment sand inferred phylogenies from the study "Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweedsNeoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds".

#----------------------#
#    SEQUENCES   #
#----------------------#

HOMCHL*.fltr.nt.fa                                        nucleotidic sequences without need of scaffolding
HOMCHL*.fltr.nt.no_scaffold.fa                            nucleotidic sequences not scaffolded
HOMCHL*.fltr.nt.scaffold.fa                                nucleotidic sequences scaffolded
HOMCHL*.fltr.aa.align.fa                                amino acid sequences without need of scaffolding
HOMCHL*.fltr.aa.align.no_scaffold.fa                    amino acid sequences not scaffolded
HOMCHL*.fltr.aa.align.scaffold.fa                        amino acid sequences scaffolded

#----------------------#
#   ALIGNMENTS  #
#----------------------#

HOMCHL*.fltr.nt.align.fa                                alignment of nucleotidic sequences without need of scaffolding
HOMCHL*.fltr.nt.no_scaffold.align.fa                    alignment of nucleotidic sequences not scaffolded
HOMCHL*.fltr.nt.scaffold.align.fa                        alignment of nucleotidic sequences scaffolded
HOMCHL*.fltr.aa.align.align.fa                            alignment of amino acid sequences without need of scaffolding
HOMCHL*.fltr.aa.align.no_scaffold.align.fa                alignment of amino acid sequences not scaffolded
HOMCHL*.fltr.aa.align.scaffold.align.fa                    alignment of amino acid sequences scaffolded
HOMCHL*.fltr.nt.align.trim.fa                            trim alignment of nucleotidic sequences without need of scaffolding
HOMCHL*.fltr.nt.no_scaffold.align.trim.fa                trim alignment of nucleotidic sequences not scaffolded
HOMCHL*.fltr.nt.scaffold.align.trim.fa                    trim alignment of nucleotidic sequences scaffolded
HOMCHL*.fltr.aa.align.align.trim.fa                        trim alignment of amino acid sequences without need of scaffolded
HOMCHL*.fltr.aa.align.no_scaffold.align.trim.fa            trim alignment of amino acid sequences not scaffolded
HOMCHL*.fltr.aa.align.scaffold.align.trim.fa            trim alignment of amino acid sequences scaffolded

#--------------------------------#
#  PHYLOGENETIC TREES  #
#--------------------------------#

allgenes_coreGF_aa_noscaffold.C20.contree                coreGF concatenated ML tree, no scaffold, C20 mixture model
allgenes_coreGF_aa_noscaffold.contree                    coreGF concatenated ML tree, no scaffold, gene-wise partition
allgenes_coreGF_aa_noscaffold.trim.C20.contree            coreGF concatenated ML tree, no scaffold, trimmed alignment, C20 mixture model
allgenes_coreGF_aa_noscaffold.trim.contree                coreGF concatenated ML tree, no scaffold, trimmed alignment, gene-wise partition
allgenes_coreGF_aa_scaffold.C20.contree                    coreGF concatenated ML tree, scaffold, C20 mixture model
allgenes_coreGF_aa_scaffold.contree                        coreGF concatenated ML tree, scaffold, gene-wise partition
allgenes_coreGF_aa_scaffold.trim.C20.contree            coreGF concatenated ML tree, scaffold, trimmed alignment, C20 mixture model
allgenes_coreGF_aa_scaffold.trim.contree                coreGF concatenated ML tree, scaffold, trimmed alignment, gene-wise partition
allgenes_UlvoGF_aa_noscaffold.C20.contree                ulvoGF concatenated ML tree, no scaffold, C20 mixture model
allgenes_UlvoGF_aa_noscaffold.contree                    ulvoGF concatenated ML tree, no scaffold, gene-wise partition
allgenes_UlvoGF_aa_noscaffold.trim.C20.contree            ulvoGF concatenated ML tree, no scaffold, trimmed alignment, C20 mixture model
allgenes_UlvoGF_aa_noscaffold.trim.contree                ulvoGF concatenated ML tree, no scaffold, trimmed alignment, gene-wise partition
allgenes_UlvoGF_aa_scaffold.C20.contree                    ulvoGF concatenated ML tree, scaffold, C20 mixture model
allgenes_UlvoGF_aa_scaffold.contree                        ulvoGF concatenated ML tree, scaffold, gene-wise partition
allgenes_UlvoGF_aa_scaffold.trim.C20.contree            ulvoGF concatenated ML tree, scaffold, trimmed alignment, C20 mixture model
allgenes_UlvoGF_aa_scaffold.trim.contree                ulvoGF concatenated ML tree, scaffold, trimmed alignment, gene-wise partition
allgenes_coreGF_aa_noscaffold.noIgn.contree                coreGF concatenated ML tree, no scaffold, gene-wise partition, Ignatius excluded
allgenes_coreGF_aa_noscaffold.trim.contree                coreGF concatenated ML tree, no scaffold, trimmed alignment, gene-wise partition, Ignatius excluded
allgenes_coreGF_aa_scaffold.noIgn.contree                coreGF concatenated ML tree, scaffold, gene-wise partition, Ignatius excluded
allgenes_coreGF_aa_scaffold.trim.contree                coreGF concatenated ML tree, scaffold, trimmed alignment, gene-wise partition, Ignatius excluded
allgenes_UlvoGF_aa_noscaffold.contree                    ulvoGF concatenated ML tree, no scaffold, gene-wise partition, Ignatius excluded
allgenes_UlvoGF_aa_noscaffold.trim.contree                ulvoGF concatenated ML tree, no scaffold, trimmed alignment, gene-wise partition, Ignatius excluded
allgenes_UlvoGF_aa_scaffold.contree                        ulvoGF concatenated ML tree, scaffold, gene-wise partition, Ignatius excluded
allgenes_UlvoGF_aa_scaffold.trim.contree                ulvoGF concatenated ML tree, scaffold, trimmed alignment, gene-wise partition, Ignatius excluded
ASTRAL_noscaffold_output.BS.tre                            coreGF coalescence-based tree, no scaffold, MLBS                    
ASTRAL_noscaffold_output.tre                            coreGF coalescence-based tree, no scaffold, BestML                    
ASTRAL_noscaffold_output.trim.BS.tre                    coreGF coalescence-based tree, no scaffold, trimmed alignment, MLBS                            
ASTRAL_noscaffold_output.trim.tre                        coreGF coalescence-based tree, no scaffold, trimmed alignment, BestML                        
ASTRAL_scaffold_output.BS.tre                            coreGF coalescence-based tree, scaffold, MLBS                    
ASTRAL_scaffold_output.tre                                coreGF coalescence-based tree, scaffold, BestML                
ASTRAL_scaffold_output.trim.BS.tre                        coreGF coalescence-based tree, scaffold, trimmed alignment, MLBS                        
ASTRAL_scaffold_output.trim.tre                            coreGF coalescence-based tree, no scaffold, trimmed alignment, BestML                    
ASTRAL_UlvoGF_noscaffold_output.BS.tre                    ulvoGF coalescence-based tree, no scaffold, MLBS                            
ASTRAL_UlvoGF_noscaffold_output.tre                        ulvoGF coalescence-based tree, no scaffold, BestML                        
ASTRAL_UlvoGF_noscaffold_output.trim.BS.tre                ulvoGF coalescence-based tree, no scaffold, trimmed alignment, MLBS                                
ASTRAL_UlvoGF_noscaffold_output.trim.tre                ulvoGF coalescence-based tree, no scaffold, trimmed alignment, BestML                                
ASTRAL_UlvoGF_scaffold_output.BS.tre                    ulvoGF coalescence-based tree, scaffold, MLBS                            
ASTRAL_UlvoGF_scaffold_output.tre                        ulvoGF coalescence-based tree, scaffold, BestML                        
ASTRAL_UlvoGF_scaffold_output.trim.BS.tre                ulvoGF coalescence-based tree, scaffold, trimmed alignment, MLBS                                
ASTRAL_UlvoGF_scaffold_output.trim.tre                    ulvoGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded
ASTRAL_noscaffold_output.BS.noIgn.tre                    coreGF coalescence-based tree, no scaffold, MLBS, Ignatius excluded
ASTRAL_noscaffold_output.noIgn.tre                        coreGF coalescence-based tree, no scaffold, BestML, Ignatius excluded
ASTRAL_noscaffold_output.BS.trim.noIgn.tre                coreGF coalescence-based tree, no scaffold, trimmed alignment, MLBS, Ignatius excluded
ASTRAL_noscaffold_output.noIgn.tre                        coreGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded
ASTRAL_scaffold_output.BS.noIgn.tre                        coreGF coalescence-based tree, scaffold, MLBS, Ignatius excluded
ASTRAL_scaffold_output.BS.trim.noIgn.tre                coreGF coalescence-based tree, scaffold, BestML, Ignatius excluded
ASTRAL_scaffold_output.noIgn.tre                        coreGF coalescence-based tree, scaffold, trimmed alignment, MLBS                        , Ignatius excluded
ASTRAL_scaffold_output.trim.noIgn.tre                    coreGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded
ASTRAL_UlvoGF_noscaffold_output.BS.noIgn.tre            ulvoGF coalescence-based tree, no scaffold, MLBS, Ignatius excluded
ASTRAL_UlvoGF_noscaffold_output.noIgn.tre                ulvoGF coalescence-based tree, no scaffold, BestML, Ignatius excluded
ASTRAL_UlvoGF_noscaffold_output.trim.BS.noIgn.tre        ulvoGF coalescence-based tree, no scaffold, trimmed alignment, MLBS, Ignatius excluded
ASTRAL_UlvoGF_noscaffold_output.trim.noIgn.tre            ulvoGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded
ASTRAL_UlvoGF_scaffold_output.BS.noIgn.tre                ulvoGF coalescence-based tree, scaffold, MLBS, Ignatius excluded
ASTRAL_UlvoGF_scaffold_output.noIgn.tre                    ulvoGF coalescence-based tree, scaffold, BestML, Ignatius excluded
ASTRAL_UlvoGF_scaffold_output.trim.BS.noIgn.tre            ulvoGF coalescence-based tree, scaffold, trimmed alignment, MLBS, Ignatius excluded
ASTRAL_UlvoGF_scaffold_output.trim.noIgn.tre            ulvoGF coalescence-based tree, no scaffold, trimmed alignment, BestML, Ignatius excluded
02_*.chronogram                                                            time-calibrated trees, consult Table S6 for details
03_*.chronogram                                                            time-calibrated trees, consult Table S6 for details_*.chronogram                                                            time-calibrated tress, consult Table S6 for details


#---------------------------------------------------------------------------------------------------------------------------------------#
# for questions and additional info regarding the datasets, please contact andrea.delcortona@gmail.com #
#----------------------------------------------------------------------------------------------------------------------------------------#

Files (311.9 MB)
Name Size
02_run_T1_ln_CAT_R0.CAT_chain_1_sample.chronogram
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02_run_T1_ln_CAT_R0.LG_chain_1_sample.chronogram
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02_run_T1_ln_CAT_R1.CAT_chain_1_sample.chronogram
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02_run_T1_ln_CAT_R1.LG_chain_1_sample.chronogram
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02_run_T1_ln_CAT_R2.CAT_chain_1_sample.chronogram
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02_run_T1_ln_CAT_R2.LG_chain_1_sample.chronogram
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02_run_T1_ln_CAT_R3.CAT_chain_1_sample.chronogram
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02_run_T1_ln_CAT_R3.LG_chain_1_sample.chronogram
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02_run_T1_ugam_CAT_R0.CAT_chain_1_sample.chronogram
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02_run_T1_ugam_CAT_R0.LG_chain_1_sample.chronogram
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02_run_T1_ugam_CAT_R1.CAT_chain_1_sample.chronogram
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2.5 kB Download
02_run_T1_ugam_CAT_R1.LG_chain_1_sample.chronogram
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02_run_T1_ugam_CAT_R2.CAT_chain_1_sample.chronogram
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2.5 kB Download
02_run_T1_ugam_CAT_R2.LG_chain_1_sample.chronogram
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2.5 kB Download
02_run_T1_ugam_CAT_R3.CAT_chain_1_sample.chronogram
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02_run_T1_ugam_CAT_R3.LG_chain_1_sample.chronogram
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2.5 kB Download
02_run_T4_ln_CAT_R0.CAT_chain_1_sample.chronogram
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02_run_T4_ln_CAT_R0.LG_chain_1_sample.chronogram
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2.5 kB Download
02_run_T4_ln_CAT_R1.CAT_chain_1_sample.chronogram
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02_run_T4_ln_CAT_R1.LG_chain_1_sample.chronogram
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2.5 kB Download
02_run_T4_ln_CAT_R2.CAT_chain_1_sample.chronogram
md5:9875fb44d342493cc142b40ed564710d
2.5 kB Download
02_run_T4_ln_CAT_R2.LG_chain_1_sample.chronogram
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02_run_T4_ln_CAT_R3.CAT_chain_1_sample.chronogram
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2.5 kB Download
02_run_T4_ln_CAT_R3.LG_chain_1_sample.chronogram
md5:1c0fb56990da83ed140513abe312868a
2.5 kB Download
02_run_T4_ugam_CAT_R0.CAT_chain_1_sample.chronogram
md5:2bdadfd057ed94fbb5c19740a6b2a756
2.5 kB Download
02_run_T4_ugam_CAT_R0.LG_chain_1_sample.chronogram
md5:eba6a1d100cfbfe4369803015473277c
2.5 kB Download
02_run_T4_ugam_CAT_R1.CAT_chain_1_sample.chronogram
md5:c1c9a3f0a652f62815e6a1fb6797a931
2.5 kB Download
02_run_T4_ugam_CAT_R1.LG_chain_1_sample.chronogram
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2.5 kB Download
02_run_T4_ugam_CAT_R2.CAT_chain_1_sample.chronogram
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2.5 kB Download
02_run_T4_ugam_CAT_R2.LG_chain_1_sample.chronogram
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2.5 kB Download
02_run_T4_ugam_CAT_R3.CAT_chain_1_sample.chronogram
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2.5 kB Download
02_run_T4_ugam_CAT_R3.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ln_CAT_R0.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ln_CAT_R0.LG_chain_1_sample.chronogram
md5:f9e855c67512fae74b415634759acf53
2.5 kB Download
03_noPr_run_T1_ln_CAT_R1.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ln_CAT_R1.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ln_CAT_R2.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ln_CAT_R2.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ln_CAT_R3.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ln_CAT_R3.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ugam_CAT_R0.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ugam_CAT_R0.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ugam_CAT_R1.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ugam_CAT_R1.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ugam_CAT_R2.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ugam_CAT_R2.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ugam_CAT_R3.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T1_ugam_CAT_R3.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ln_CAT_R0.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ln_CAT_R0.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ln_CAT_R1.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ln_CAT_R1.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ln_CAT_R2.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ln_CAT_R2.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ln_CAT_R3.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ln_CAT_R3.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ugam_CAT_R0.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ugam_CAT_R0.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ugam_CAT_R1.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ugam_CAT_R1.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ugam_CAT_R2.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ugam_CAT_R2.LG_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ugam_CAT_R3.CAT_chain_1_sample.chronogram
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2.5 kB Download
03_noPr_run_T4_ugam_CAT_R3.LG_chain_1_sample.chronogram
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2.5 kB Download
allgenes_coreGF_aa_noscaffold.C20.contree
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allgenes_coreGF_aa_noscaffold.contree
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allgenes_coreGF_aa_noscaffold.noIgn.contree
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allgenes_coreGF_aa_noscaffold.trim.C20.contree
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allgenes_coreGF_aa_noscaffold.trim.contree
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allgenes_coreGF_aa_noscaffold.trim.noIgn.contree
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allgenes_coreGF_aa_scaffold.C20.contree
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allgenes_coreGF_aa_scaffold.contree
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