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+# Changelog
+
+
+## v0.3.5
+Nov 22 2019
+
+   - better reporting when filtering of abundant satellite is used
+   - number of changes in names of output files - file names are now more informative. Changes include:
+   
+| old file name                                                            | new file name                                                        |
+|--------------------------------------------------------------------------|----------------------------------------------------------------------|
+| TR_consensus_rank_1_.fasta                                               | TAREAN_consensus_rank_1.fasta                                        |
+| TR_consensus_rank_2_.fasta                                               | TAREAN_consensus_rank_2.fasta                                        |
+| TR_consensus_rank_3_.fasta                                               | TAREAN_consensus_rank_3.fasta                                        |
+| TR_consensus_rank_4_.fasta                                               | TAREAN_consensus_rank_4.fasta                                        |
+| sequences/sequences.fasta                                                | reads/reads.fasta                                                    |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info.minRD5_sort-GR     | clustering/clusters/dir_CL0001/contigs.info.minRD5_sort-GR.fasta     |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info.minRD5_sort-length | clustering/clusters/dir_CL0001/contigs.info.minRD5_sort-length.fasta |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info.minRD5             | clustering/clusters/dir_CL0001/contigs.info.minRD5_sort-RD.fasta     |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.aln.profile                 | clustering/clusters/dir_CL0001/contigs.profile                       |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.aln.info                    | clustering/clusters/dir_CL0001/contigs.info.fasta                    |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.ace                         | clustering/clusters/dir_CL0001/contigs.ace                           |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.contigs.qual                | clustering/clusters/dir_CL0001/contigs.qual                          |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.aln                         | clustering/clusters/dir_CL0001/contigs.aln                           |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.contigs                     | clustering/clusters/dir_CL0001/contigs.fasta                         |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.info                        | clustering/clusters/dir_CL0001/assembly.info                         |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.singlets                    | clustering/clusters/dir_CL0001/singlets.fasta                        |
+| clustering/clusters/dir_CL0001/reads.fas.CL1.contigs.links               | clustering/clusters/dir_CL0001/contigs.links                         |
+| clustering/clusters/dir_CL0001/reads_oriented.fas                        | clustering/clusters/dir_CL0001/reads_selection_oriented.fasta        |
+| clustering/clusters/dir_CL0001/CL1_directed_graph.RData.                 | clustering/clusters/dir_CL0001/graph_layout_directed.RData           |
+| clustering/clusters/dir_CL0001/CL1_tmb.png                               | clustering/clusters/dir_CL0001/graph_layout_tmb.png                  |
+| clustering/clusters/dir_CL0001/CL1.png                                   | clustering/clusters/dir_CL0001/graph_layout.png                      |
+| clustering/clusters/dir_CL0001/CL1.GL                                    | clustering/clusters/dir_CL0001/graph_layout.GL                       |
+| clustering/clusters/dir_CL0001/blast.csv                                 | clustering/clusters/dir_CL0001/hitsort_part.csv                      |
+
+## v0.3.4
+Oct 31 2019
+
+  - Classification of superclusters improved, classification now uses information about LTR/PBS for classification of Class_I elements
+  
+
+## v0.3.2
+Oct 9 2019
+
+  - Graphical reporting of comparative analysis added 
+
+## v0.3.1
+Jan 9 2019
+
+  - Improved detection of low complexity repeats and satellites with shorter monomer
+
+## v0.3.0
+Oct 25 2018
+
+ - For back-compatibility, it is possible to select protein database version
+ - Databases of protein domains went public 
+
+## v0.2.10
+Oct 24 2018
+
+ - Protein database for Viridiplantae updated
+
+## v0.2.9
+Jan 3 2018
+
+ - read depth for contigs is calculated
+ - contigs are also sorted based on genome representation
+ 
+## v0.2.8
+Dec 18 2017
+
+ - by default assembly is done on clusters with size at least 5 reads
+ - preset option of Illumina, Illumina short and Oxford Nanopore
+ - option for analyzing Metazoa/ Viridiplantae added
+ - protein databases can be obtained **using fetch_databases.sh** script (password required)
+
+## v0.2.7
+Dec 05 2017
+
+ - improved DNA database - protein domain were masked not to interfere with protein domain database
+ - another bug fix in parallelization and assembly 
+ - alternative to blastx added - DIAMOND program can be used instead
+ 
+## v0.2.6
+Nov 14 2017
+
+- Improved classification of superclusters
+- tables in HTML reports improved
+- assembly is performed on low confidence satellite sequences
+- assembly optimized, bug fix in parallelization
+
+## v0.2.5
+Sep 1 2017
+
++ More options added to _galaxy interface_ of TAREAN and RepeatExplorer2:
+    - automatic satellite filtering
+    - cluster size threshold setting
+    - keep original sequence names option
++ Pipeline tests added
+
+## v0.2.4
+Aug 10 2017
+
+- Filtering of abundant satellite sequences
+- Improved (more sensitive) search of protein domains 
+- bug fix in parallelization
+- SHORT_ILLUMINA option added, this enable to analyze shorter reads (50nt) - command line only
+- OXFORD_NANOPORE option added (experimental feature, command line only)
+
+## v0.2.3
+Jun 9 2017
+
+- some changes in standalone TAREAN
+
+## v0.2.2
+
+- improved visualization of comparative analysis 
+
+## v0.2.1
+
+- log file is automatically copied to output and is part of archive(in galaxy)
+
+## v0.2.0
+
++ Improved HTML output
++ Updated documentation
++ Full clustering analysis - RepeatExplorer2
++ New features:
+    - Cap3 assembly added
+    - Comparative analysis
+    - LTR detection from contigs
+    - Custom database option
+    - Bugfix in excessive CPU usage
+    - Detection of TE protein domains
+
+## v0.1.1
+
++ New features:
+    - Cluster merging
+    - Scan of clusters against DNA database (detection of rDNA, plastid, mitochondrial and contaminants)
+
+## v0.1.0
+
+
+