test_data

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tests...

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    ./clade_analysis_test_1.xml
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    ./clade_analysis_test_2.xml
minor improvements and bug-fixes

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    ./phyloxml_test_1.xml
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fixed issue with UTF8 encoding.

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more tests for isDuplication() and isSpecation() added

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allow confidence values of 0.0 for domains minor bug fixes clean up

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inprogress

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temp

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    ./spec_test_1.xml
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iterating nexus test

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    ./nexus_test_4_1.nex
iterating nh parser

ancestor analysis fails on this

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    ./amphi_frost.xml
"rio" work

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    ./rio_mb_taxcode.run1.t
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    ./rio_mb_taxcode_1.run1.t
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    ./rio_mb_taxcode_2.run1.t
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    ./rio_mb_taxid.run1.t
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    ./rio_mb_taxsn.run1.t
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    ./rio_tol_1.xml
not needed

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    ./Bcl-2_e1_20_mafft_05_40_fme.mlt
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    ./Bcl-2_e1_20_mafft_05_40_fme.xml
rio

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    ./rio_Bcl-2_e1_20_mafft_05_40_fme.mlt
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    ./rio_Bcl-2_e1_20_mafft_05_40_fme.xml
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    ./rio_species.xml
"rio" work

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    ./Bcl-2_e1_20_mafft_05_40_fme.mlt
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    ./Bcl-2_e1_20_mafft_05_40_fme.xml
in progress

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    ./gsdi_test_gene_tree_codes.xml
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    ./gsdi_test_gene_tree_ids.xml
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    ./gsdi_test_gene_tree_sn.xml
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    ./gsdi_test_gene_tree_sn_wnt.xml
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    ./gsdi_test_species_tree.xml
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    ./gsdi_test_species_tree_codes.nh
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    ./gsdi_test_species_tree_codes.xml
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    ./gsdi_test_species_tree_ids.xml
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    ./gsdi_test_species_tree_sn.nh
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    ./gsdi_test_species_tree_sn.xml
new tol

fixed

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    ./gene_tree_tax_code_4.xml
phylotastic hackathon at NESCENT 120608

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    ./wnt_psiblast_tree_seq_ids.nwk
phylotastic hackathon at NESCENT 120606

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    ./wnt_gene_tree_from_ncbi_blast.nh
more test data added

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    ./Bininda-emonds_2007_mammals.nex
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    ./Smith_2011_angiosperms.nh
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    ./Westneat_Lundberg_BigFishTree.nex