IQ-TREE - Efficient software for phylogenomic inference Location and version:
1 2 3 4 5 6 $ which iqtree2 /local/cluster/bin/iqtree2 $ iqtree2 --version IQ-TREE multicore version 2.1.3 COVID-edition for Linux 64-bit built Apr 21 2021 Developed by Bui Quang Minh, James Barbetti, Nguyen Lam Tung, Olga Chernomor, Heiko Schmidt, Dominik Schrempf, Michael Woodhams. help message:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 $ iqtree2 --help IQ-TREE multicore version 2.
SPAdes – St. Petersburg genome assembler SPAdes is an assembly toolkit containing various assembly pipelines
Location and version:
1 2 3 4 $ which spades.py /local/cluster/SPAdes/bin/spades.py $ spades.py --version SPAdes genome assembler v3.15.3 help message:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 $ spades.
MAFFT version 7 - Multiple alignment program for amino acid or nucleotide sequences Location and version:
1 2 3 4 $ which mafft /local/cluster/mafft/bin/mafft $ mafft --version v7.487 (2021/Jul/25) help message:
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 $ mafft --help ------------------------------------------------------------------------------ MAFFT v7.487 (2021/Jul/25) https://mafft.cbrc.jp/alignment/software/ MBE 30:772-780 (2013), NAR 30:3059-3066 (2002) ------------------------------------------------------------------------------ High speed: % mafft in > out % mafft --retree 1 in > out (fast) High accuracy (for <~200 sequences x <~2,000 aa/nt): % mafft --maxiterate 1000 --localpair in > out (% linsi in > out is also ok) % mafft --maxiterate 1000 --genafpair in > out (% einsi in > out) % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out) If unsure which option to use: % mafft --auto in > out --op # : Gap opening penalty, default: 1.
BLAST DBs (nr and nt) have been updated.
You will be able to use these if your $BLASTDB is properly set, which should be done for you automatically. If you need to use nt or nr, you can use them by specifying blastn -db nt or blastp -db nr as necessary.
Location and version:
1 2 3 /nfs1/CGRB/databases/NCBI/v5/blast_20210726 $ echo $BLASTDB /nfs1/CGRB/BlastDB/NCBI/v5/latest_blast_DB A nr database for DIAMOND can be found here: /nfs1/CGRB/databases/NCBI/latest_diamond_DB/nr.
DIAMOND - Fast and sensitive protein alignment DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are:
Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST. Frameshift alignments for long read analysis. Low resource requirements and suitable for running on standard desktops or laptops. Various output formats, including BLAST pairwise, tabular and XML, as well as taxonomic classification.
funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). Installation, usage, and more information can be found at http://funannotate.readthedocs.io
To activate, check out a node with qrsh and run:
1 2 bash source /local/cluster/funannotate/activate.sh To use in SGE_Batch, write a shell script that includes the above source line, then the commands you would like to run.
Location and version:
