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Commits on Sep 29, 2025

• improved readme

  qjiangzhao

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  e8edd16

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Commits on Sep 26, 2025

• add TEtrimmer paper to readme

  qjiangzhao

  committed
  578f9d1

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Commits on Sep 24, 2025

• added standard output for the test file

  qjiangzhao

  committed
  ccb0005

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• add TEtrimmer version number into the log file

  qjiangzhao

  committed
  bc0f283

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Commits on Sep 23, 2025

• fixed LINE poly end error, changed raw manual check file

  qjiangzhao

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  88aedcc

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Commits on Sep 22, 2025

• test

  qjiangzhao

  committed
  63f6247

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• format

  qjiangzhao

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  e90b5aa

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Commits on Sep 4, 2025

• fixed TE-Aid protein domain plot error

  qjiangzhao

  committed
  570dba0

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Commits on Sep 3, 2025

• decrease the threshold for consensus sequence generation for the extended TE-Aid plot

  qjiangzhao

  committed
  20c17dd

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• remove DEBUG logging

  qjiangzhao

  committed
  2b7557b

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Commits on Aug 17, 2025

• change logging INFO color to the default terminal text color

  qjiangzhao

  committed
  7b36a47

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Commits on Aug 13, 2025

• don't use LTR or TIR to define boundaries for Penelope DIRS and CACTA elements

  qjiangzhao

  committed
  d355071

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• modified readme

  qjiangzhao

  committed
  504727f

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• name new release to 1.5.4

  qjiangzhao

  committed
  cd66e14

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• upgrate to 1.5.3

  qjiangzhao

  committed
  b019d03

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• modified TE-Aid plots, start 0 from the biginning of axis

  qjiangzhao

  committed
  f40f744

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Commits on Aug 12, 2025

• fixed low_copy TE-Aid bug

  qjiangzhao

  committed
  8e277ea

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• add one more TE-Aid plot for extended MSA

  qjiangzhao

  committed
  e5806f5

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Commits on Aug 11, 2025

• fixed pdf merge bug for low_copy TEs

  qjiangzhao

  committed
  d6f0eaf

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• fixed ta-aid check_blast bug

  qjiangzhao

  committed
  958aef8

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• fixed check_blast_full_length bug

  qjiangzhao

  committed
  d2c62f2

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• fixed repeatmasker repeatmodeler dependencies checking bug for linux system

  qjiangzhao

  committed
  8b7a235

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• delete temp

  qjiangzhao

  committed
  266a000

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• updated tetrimmer verstion to 1.5.2

  qjiangzhao

  committed
  54df789

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• add cluster_identity to summary.txt

  qjiangzhao

  committed
  fdbd6c6

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• integrate cluster number into summary.txt

  qjiangzhao

  committed
  c192c74

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• add helitron patterns options

  qjiangzhao

  committed
  8f15666

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Commits on Aug 10, 2025

• add helitron ends check function

  qjiangzhao

  committed
  be751b0

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Commits on Aug 9, 2025

• Improve readme

  qjiangzhao

  committed
  1cfaf44

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Commits on Aug 8, 2025

• sort cluster by TE genome coverate percentage, add evaluation and TE type to cluster name

  qjiangzhao

  committed
  a374728

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• add input_genome_cov_len and output_genome_cov_len to summary.txt

  qjiangzhao

  committed
  6407665

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• add gapopen column to blast

  qjiangzhao

  committed
  16e6193

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• improved summary file add three more columns including identify input_coverage and output_coverage

  qjiangzhao

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  c38e318

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Commits on Aug 7, 2025

• add input output TE sequence identity into summary file

  qjiangzhao

  committed
  1007cc1

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• improved TEAid functions

  qjiangzhao

  committed
  40d159a

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